Intrepreting the results
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The goal of SelectSim package is to implement the methodology to infer inter-dependencies between functional alterations in cancer. SelectSim estimates the expected number of mutations in a given gene and a given sample from the mutation frequency of the gene, f(g), and the tumor mutation burden (TMB) of the sample, μ (t). These values can be estimated within specific mutation and tumor subsets, to account for heterogeneous tumor types, tissue specificities, and distinct mutational processes
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SelectSim Method
Installation
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articles:
data_processing: data_processing.html
introduction: introduction.html
-last_built: 2024-08-23T11:08Z
+last_built: 2024-08-23T11:19Z
urls:
reference: https://csogroup.github.io/SelectSim/reference
article: https://csogroup.github.io/SelectSim/articles
diff --git a/docs/search.json b/docs/search.json
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-[{"path":"https://csogroup.github.io/SelectSim/INSTALLATION.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"NA","text":"can install development version SelectSim GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/INSTALLATION.html","id":"installation-with-micromamba-enviorment","dir":"","previous_headings":"","what":"Installation with micromamba enviorment","title":"NA","text":"micromamba tiny version mamba package manager (Like Conda). Refer website ’s installation guide. Steps follow installing micromamba terminal: micromamba create -n r_env r-essentials r-base micromamba activate r_env micromamba install conda-forge::r-devtools micromamba install conda-forge::armadillo micromamba install conda-forge::r-rcppparallel micromamba install conda-forge::r-rfast run R install SelectSim R package follows Alternative way install provided enviorment.yml file. micromamba create -f env.yml micromamba activate r_env - run R install SelectSim R package follows","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE) # install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 SelectSim authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Data_processing","text":"can install development version SelectSim GitHub : details installation refer INSTALLATION","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Data_processing","text":"process LUAD MAF dataset TCGA provided package. also use oncokb v3.9 cancer genes mutations filter maf create gam provided pacakge. NOTE: example prcoess MAF file. know prcossed MAF file run_data object, please refer SelectSim_analysis repository. Let print number lines number samples Let create table schema mutations conisder columns defined maf file Number samples maf file Filter maf file include oncokb cancer genes","code":"library(SelectSim) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(tictoc) ## Load the data provided with the package data(luad_maf, package = \"SelectSim\") data(oncokb_genes, package = \"SelectSim\") data(oncokb_truncating_genes, package = \"SelectSim\") data(variant_catalogue, package = \"SelectSim\") # Check the MAF dim(luad_maf) #> [1] 220734 8 input_maf <- luad_maf print(paste('##### Number of lines ####',nrow(input_maf),sep=\"->\")) #> [1] \"##### Number of lines ####->220734\" genes_to_consider = oncokb_genes print(paste('##### Number of genes ####',length(genes_to_consider),sep=\"->\")) #> [1] \"##### Number of genes ####->396\" mutation_type = list( 'ignore' = c(\"Silent\",\"Intron\",\"RNA\",\"3'UTR\",\"5'UTR\",\"5'Flank\",\"3'Flank\",\"IGR\"), 'truncating'= c('Frame_Shift_Del','Frame_Shift_Ins','In_Frame_Del','In_Frame_Ins','Nonsense_Mutation','Nonstop_Mutation','Splice_Region','Splice_Site','Translation_Start_Site'), 'missense' = c('Missense_Mutation') ) custom_maf_schema = list( 'name' = 'custom_maf', 'column' = list( 'gene' = 'Hugo_Symbol' , 'gene.name' = 'Hugo_Symbol' , 'sample' = 'sample' , 'sample.name' = 'sample' , 'mutation.type' = 'Variant_Classification' , 'mutation' = 'HGVSp_Short' ), 'mutation.type' = mutation_type ) mut_samples = unique(input_maf[, custom_maf_schema$column$sample]) print(paste('##### Number of samples ####',length(mut_samples),sep=\"->\")) #> [1] \"##### Number of samples ####->502\" maf_genes = filter_maf_gene.name(input_maf, genes = genes_to_consider, gene.col = custom_maf_schema$column$gene) print(paste('##### Number of lines ####',nrow(maf_genes),sep=\"->\")) #> [1] \"##### Number of lines ####->6708\""},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"genrating-the-gams","dir":"Articles","previous_headings":"Example","what":"Genrating the GAMs","title":"Data_processing","text":"generate GAM consider genes consider truncating mutations. also create TMB dataframe takes truncating mutation genes consideration. generate GAM genes hotspot mutations oncokb v3.9. also create TMB dataframe takes Missense mutation genes consideration.","code":"# Creating Truncating GAM tic('##### Creating Truncating GAM ####') maf_trunc = filter_maf_truncating(maf_genes,genes=oncokb_truncating_genes, custom_maf_schema) input_maf_trunc<-filter_maf_truncating(input_maf, custom_maf_schema) truncating_tmb <- data.frame('sample'=mut_samples,'mutation'=rep(0,length(mut_samples))) rownames(truncating_tmb)<-mut_samples temp <- input_maf_trunc %>% count(sample) rownames(temp)<-temp$sample truncating_tmb[intersect(truncating_tmb$sample,temp$sample),]$mutation <-temp[intersect(truncating_tmb$sample,temp$sample),'n'] tcga_truc_gam = maf2gam(maf_trunc, sample.col = custom_maf_schema$column$sample, gene.col = custom_maf_schema$column$gene, value.var = 'Variant_Classification', samples = mut_samples, genes = genes_to_consider, fun.aggregate = length, binarize=TRUE, fill=0) truncating_data <- list('gam'=tcga_truc_gam, 'tmb'=truncating_tmb) toc() #> ##### Creating Truncating GAM ####: 0.214 sec elapsed # Creating Missense GAM tic('##### Creating Missense GAM ####') maf_valid = filter_maf_schema(input_maf, schema = custom_maf_schema, column = 'mutation.type', values = custom_maf_schema[['mutation.type']][['ignore']], inclusive = FALSE) missense_maf<-filter_maf_mutation.type(input_maf, variants = 'Missense_Mutation', variant.col = custom_maf_schema$column$mutation.type) missense_tmb <- data.frame('sample'=mut_samples,'mutation'=rep(0,length(mut_samples))) rownames(missense_tmb)<-mut_samples temp <- missense_maf %>% count(sample) rownames(temp)<-temp$sample missense_tmb[intersect(missense_tmb$sample,temp$sample),]$mutation <-temp[intersect(missense_tmb$sample,temp$sample),'n'] t_m = substr(maf_valid[[custom_maf_schema$column$mutation]],3,1000) t_m1 = gsub('[A-Z]*$', '', t_m) maf_valid$HGVSp_Short_fixed = t_m1 maf_hotspot = filter_maf_mutations(maf_valid, variant_catalogue, maf.col = c(custom_maf_schema$column$gene, 'HGVSp_Short_fixed'), values.col = c('gene', 'mut')) missense_tcga_gam = maf2gam(maf_hotspot, sample.col = custom_maf_schema$column$sample, gene.col = custom_maf_schema$column$gene, value.var = 'Variant_Classification', samples = mut_samples, genes = genes_to_consider, fun.aggregate = length, binarize=TRUE, fill=0) missesne_data <- list('gam'=missense_tcga_gam, 'tmb'=missense_tmb) toc() #> ##### Creating Missense GAM ####: 1.706 sec elapsed"},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"genrating-the-run_object-to-run-selectx","dir":"Articles","previous_headings":"Example","what":"Genrating the run_object to run SelectX","title":"Data_processing","text":"M: list object GAMs presence absence matrix alterations tmb: list object tumor mutation burden data frame column names () sample mutationn sample.class named vector sample annotations alteration.class named vector alteration annotations Save run_data check introduction vignette see run selectX discover EDs.","code":"gene_to_take <- colnames(missesne_data$gam) order <- rownames(missesne_data$gam) data <-list('M'=list('missense'=t(missesne_data$gam[order,gene_to_take]), 'truncating'=t(truncating_data$gam[rownames(missesne_data$gam[order,]),gene_to_take])), 'tmb'=list('missense'=missesne_data$tmb[order,], 'truncating'=truncating_data$tmb[order,])) alteration_covariates <- rep('MUT',ncol(missesne_data$gam[order,gene_to_take])) names(alteration_covariates)<-colnames(missesne_data$gam[order,gene_to_take]) sample_covariates<-rep('LUAD',length(order)) names(sample_covariates)<-order run_data <- list('M'=data,'sample.class' = sample_covariates,'alteration.class' = alteration_covariates) str(run_data) #> List of 3 #> $ M :List of 2 #> ..$ M :List of 2 #> .. ..$ missense : num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ATM\" \"BRAF\" \"CDKN2A\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. ..$ truncating: num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ATM\" \"BRAF\" \"CDKN2A\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> ..$ tmb:List of 2 #> .. ..$ missense :'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 163 253 270 1328 100 ... #> .. ..$ truncating:'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 24 45 40 206 17 18 73 31 176 108 ... #> $ sample.class : Named chr [1:502] \"LUAD\" \"LUAD\" \"LUAD\" \"LUAD\" ... #> ..- attr(*, \"names\")= chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> $ alteration.class: Named chr [1:396] \"MUT\" \"MUT\" \"MUT\" \"MUT\" ... #> ..- attr(*, \"names\")= chr [1:396] \"AKT1\" \"ATM\" \"BRAF\" \"CDKN2A\" ..."},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"Data_processing","text":"","code":"# Print the sessionInfo sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-conda-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /mnt/ndata/arvind/envs/R_4/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> time zone: Europe/Zurich #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] tictoc_1.2 dplyr_1.1.4 SelectSim_0.0.1.3 #> #> loaded via a namespace (and not attached): #> [1] gtable_0.3.4 xfun_0.41 bslib_0.6.1 ggplot2_3.4.4 #> [5] rstatix_0.7.2 lattice_0.22-5 vctrs_0.6.5 tools_4.3.2 #> [9] generics_0.1.3 parallel_4.3.2 tibble_3.2.1 fansi_1.0.6 #> [13] pkgconfig_2.0.3 Matrix_1.6-5 desc_1.4.3 ggridges_0.5.5 #> [17] rngtools_1.5.2 RcppParallel_5.1.6 lifecycle_1.0.4 compiler_4.3.2 #> [21] stringr_1.5.1 textshaping_0.3.7 munsell_0.5.0 codetools_0.2-19 #> [25] carData_3.0-5 htmltools_0.5.7 sass_0.4.8 yaml_2.3.8 #> [29] pillar_1.9.0 pkgdown_2.0.7 car_3.1-2 ggpubr_0.6.0 #> [33] jquerylib_0.1.4 tidyr_1.3.0 cachem_1.0.8 doRNG_1.8.6 #> [37] iterators_1.0.14 abind_1.4-5 foreach_1.5.2 tidyselect_1.2.0 #> [41] digest_0.6.34 stringi_1.8.3 reshape2_1.4.4 purrr_1.0.2 #> [45] fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0 cli_3.6.2 #> [49] magrittr_2.0.3 Rfast_2.1.0 utf8_1.2.4 broom_1.0.5 #> [53] scales_1.3.0 backports_1.4.1 RcppZiggurat_0.1.6 rmarkdown_2.25 #> [57] ggsignif_0.6.4 ragg_1.2.7 memoise_2.0.1 evaluate_0.23 #> [61] knitr_1.45 doParallel_1.0.17 rlang_1.1.3 Rcpp_1.0.12 #> [65] glue_1.7.0 jsonlite_1.8.8 R6_2.5.1 plyr_1.8.9 #> [69] systemfonts_1.0.5 fs_1.6.3"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"can install development version SelectSim GitHub : details installation refer INSTALLATION","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"run SelectSim algorithm processed LUAD dataset TCGA provided package. Note: example running processed data. Check vignette process data create run_data object needed input SelectSim algorithm.","code":"library(SelectSim) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union ## Load the data provided with the package data(luad_run_data, package = \"SelectSim\")"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"data-description-format","dir":"Articles","previous_headings":"Example","what":"Data Description & Format","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"M: list object GAMs presence absence matrix alterations tmb: list object tumor mutation burden data frame column names () sample mutationn sample.class named vector sample annotations alteration.class named vector alteration annotations","code":"# Check the data strucutre str(luad_run_data) #> List of 3 #> $ M :List of 2 #> ..$ M :List of 2 #> .. ..$ missense : num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ALK\" \"APC\" \"AR\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. ..$ truncating: num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ALK\" \"APC\" \"AR\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> ..$ tmb:List of 2 #> .. ..$ missense :'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 163 253 270 1328 100 ... #> .. ..$ truncating:'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 24 45 40 206 17 18 73 31 176 108 ... #> $ sample.class : Named chr [1:502] \"LUAD\" \"LUAD\" \"LUAD\" \"LUAD\" ... #> ..- attr(*, \"names\")= chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> $ alteration.class: Named chr [1:396] \"MUT\" \"MUT\" \"MUT\" \"MUT\" ... #> ..- attr(*, \"names\")= chr [1:396] \"AKT1\" \"ALK\" \"APC\" \"AR\" ..."},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"running-selectx","dir":"Articles","previous_headings":"Example","what":"Running SelectX","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"use function selectX() generates background model results. M: list object GAMs & TMB sample.class: named vector samples covariates alteration.class: named vector alteration covariates min.freq: Number samples gene mutated atleast n.permut: Number simulation lambda: Penalty factor used computing penalty vector tao: Fold chnage factor used computing penalty vector maxFDR: FDR rate call significnat results function returns list object contains background model results.","code":"result_obj<- selectX( M = luad_run_data$M, sample.class = luad_run_data$sample.class, alteration.class = luad_run_data$alteration.class, n.cores = 1, min.freq = 10, n.permut = 1000, lambda = 0.3, tao = 1, save.object = FALSE, verbose = FALSE, estimate_pairwise = FALSE, maxFDR = 0.25) #> Total Time: 4.371 sec elapsed"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"intrepreting-the-results","dir":"Articles","previous_headings":"Example","what":"Intrepreting the results","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"Lets look results","code":"head(result_obj$result[,1:10],n=5) #> SFE_1 SFE_2 name support_1 support_2 freq_1 freq_2 #> KRAS - TP53 KRAS TP53 KRAS - TP53 154 221 0.30677291 0.4402390 #> EGFR - KRAS EGFR KRAS EGFR - KRAS 57 154 0.11354582 0.3067729 #> STK11 - TP53 STK11 TP53 STK11 - TP53 59 221 0.11752988 0.4402390 #> BRAF - KRAS BRAF KRAS BRAF - KRAS 35 154 0.06972112 0.3067729 #> KRAS - STK11 KRAS STK11 KRAS - STK11 154 59 0.30677291 0.1175299 #> overlap w_overlap max_overlap #> KRAS - TP53 49 35.8760174 154 #> EGFR - KRAS 0 0.0000000 57 #> STK11 - TP53 13 9.5456386 59 #> BRAF - KRAS 2 0.9821429 35 #> KRAS - STK11 28 25.9230769 59"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"filtering-significant-hits","dir":"Articles","previous_headings":"Example > Intrepreting the results","what":"Filtering significant hits","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"","code":"# Filtering significant hits and counting EDs result_obj$result %>% filter(nFDR2<=0.25) %>% head(n=2) #> SFE_1 SFE_2 name support_1 support_2 freq_1 freq_2 #> KRAS - TP53 KRAS TP53 KRAS - TP53 154 221 0.3067729 0.4402390 #> EGFR - KRAS EGFR KRAS EGFR - KRAS 57 154 0.1135458 0.3067729 #> overlap w_overlap max_overlap freq_overlap r_overlap w_r_overlap #> KRAS - TP53 49 35.87602 154 0.3181818 99.02908 58.69631 #> EGFR - KRAS 0 0.00000 57 0.0000000 31.22148 16.85637 #> wES wFDR nES mean_r_nES nFDR cum_freq nFDR2 type FDR #> KRAS - TP53 -16.13638 0 -14.18270 -1.953683 0 375 0 ME TRUE #> EGFR - KRAS -11.91926 0 -10.72977 -1.189488 0 211 0 ME TRUE result_obj$result %>% filter(nFDR2<=0.25) %>% count(type) #> type n #> 1 CO 13 #> 2 ME 30"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"plotting-a-scatter-plot-of-co-mutation","dir":"Articles","previous_headings":"Example > Intrepreting the results","what":"Plotting a scatter plot of co-mutation","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"","code":"# Filtering significant hits and plotting options(repr.plot.width = 7, repr.plot.height = 7) obs_exp_scatter(result = result_obj$result,title = 'TCGA LUAD')"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"","code":"# Print the sessionInfo sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-conda-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /mnt/ndata/arvind/envs/R_4/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> time zone: Europe/Zurich #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] dplyr_1.1.4 SelectSim_0.0.1.3 #> #> loaded via a namespace (and not attached): #> [1] gtable_0.3.4 xfun_0.41 bslib_0.6.1 ggplot2_3.4.4 #> [5] rstatix_0.7.2 lattice_0.22-5 vctrs_0.6.5 tools_4.3.2 #> [9] generics_0.1.3 parallel_4.3.2 tibble_3.2.1 fansi_1.0.6 #> [13] highr_0.10 pkgconfig_2.0.3 Matrix_1.6-5 desc_1.4.3 #> [17] ggridges_0.5.5 rngtools_1.5.2 RcppParallel_5.1.6 lifecycle_1.0.4 #> [21] farver_2.1.1 compiler_4.3.2 stringr_1.5.1 tictoc_1.2 #> [25] textshaping_0.3.7 munsell_0.5.0 codetools_0.2-19 carData_3.0-5 #> [29] htmltools_0.5.7 sass_0.4.8 yaml_2.3.8 pillar_1.9.0 #> [33] pkgdown_2.0.7 car_3.1-2 ggpubr_0.6.0 jquerylib_0.1.4 #> [37] tidyr_1.3.0 cachem_1.0.8 doRNG_1.8.6 iterators_1.0.14 #> [41] abind_1.4-5 foreach_1.5.2 tidyselect_1.2.0 digest_0.6.34 #> [45] stringi_1.8.3 reshape2_1.4.4 purrr_1.0.2 fastmap_1.1.1 #> [49] grid_4.3.2 colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3 #> [53] Rfast_2.1.0 utf8_1.2.4 broom_1.0.5 withr_3.0.0 #> [57] scales_1.3.0 backports_1.4.1 RcppZiggurat_0.1.6 rmarkdown_2.25 #> [61] ggsignif_0.6.4 ragg_1.2.7 memoise_2.0.1 evaluate_0.23 #> [65] knitr_1.45 doParallel_1.0.17 rlang_1.1.3 Rcpp_1.0.12 #> [69] glue_1.7.0 jsonlite_1.8.8 R6_2.5.1 plyr_1.8.9 #> [73] systemfonts_1.0.5 fs_1.6.3"},{"path":"https://csogroup.github.io/SelectSim/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Arvind Iyer. Author, maintainer. Marco Mina. Author. Giovanni Ciriello. Author.","code":""},{"path":"https://csogroup.github.io/SelectSim/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Iyer , Mina M, Ciriello G (2024). SelectSim: Selected Events Linked Evolutionary Conditions across human Tumors. R package version 0.0.1.3, https://csogroup.github.io/SelectSim/.","code":"@Manual{, title = {SelectSim: Selected Events Linked by Evolutionary Conditions across human Tumors}, author = {Arvind Iyer and Marco Mina and Giovanni Ciriello}, year = {2024}, note = {R package version 0.0.1.3}, url = {https://csogroup.github.io/SelectSim/}, }"},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"selectsim-","dir":"","previous_headings":"","what":"Selected Events Linked by Evolutionary Conditions across human Tumors","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"goal SelectSim package implement methodology infer inter-dependencies functional alterations cancer. SelectSim estimates expected number mutations given gene given sample mutation frequency gene, f(g), tumor mutation burden (TMB) sample, μ(t). values can estimated within specific mutation tumor subsets, account heterogeneous tumor types, tissue specificities, distinct mutational processes SelectSim Method","code":""},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"can install development version SelectSim GitHub : details installation refer INSTALLATION","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"Check Vignettes folder visit website","code":""},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"who-do-i-talk-to","dir":"","previous_headings":"Example","what":"Who do I talk to?","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"bugs feature support using SelectSim, please use issue tracker. question related SelectSim, please contact Prof Giovanni Ciriello (giovanni.ciriello@unil.ch) Arvind Iyer (arvind.iyer@unil.ch).","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/GENIE_maf_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","title":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","text":"GENIE_maf_schema: GENIE_maf_schema: schema TCGA maf file process mutations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/GENIE_maf_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","text":"","code":"GENIE_maf_schema"},{"path":"https://csogroup.github.io/SelectSim/reference/GENIE_maf_schema.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","text":"object class list length 2.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/TCGA_maf_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","title":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","text":"TCGA_maf_schema: schema TCGA maf file process mutations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/TCGA_maf_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","text":"","code":"TCGA_maf_schema"},{"path":"https://csogroup.github.io/SelectSim/reference/TCGA_maf_schema.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","text":"object class list length 3.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — add","title":"Compute weight overlap stats — add","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — add","text":"","code":"add(x)"},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — add","text":"x alteration matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — add","text":"average","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — al.pairwise.alteration.stats","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"","code":"al.pairwise.alteration.stats(al, als = NULL, do.blocks = FALSE)"},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"al alteration landscape object als alteration stats object .blocks blockwise comptutation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration stats object — al.stats","title":"Create an alteration stats object — al.stats","text":"Create alteration stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration stats object — al.stats","text":"","code":"al.stats(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration stats object — al.stats","text":"al alteration landscape object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration stats object — al.stats","text":"als alteration landscape stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — am.pairwise.alteration.coverage","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"","code":"am.pairwise.alteration.coverage(overlap_M, M.stats, w_overlap_M)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"overlap_M overlap matrix M.stats matrix statis w_overlap_M weighted overlap matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"stats matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute overlap stats — am.pairwise.alteration.overlap","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"Compute overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"","code":"am.pairwise.alteration.overlap(am)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"alteration matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"overlap overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration matrix stats object — am.stats","title":"Create an alteration matrix stats object — am.stats","text":"Create alteration matrix stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration matrix stats object — am.stats","text":"","code":"am.stats(am)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration matrix stats object — am.stats","text":"alteration matrix stat object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration matrix stats object — am.stats","text":"AMS object basic stats matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"","code":"am.weight.pairwise.alteration.overlap(am, W)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"alteration matrix W weight matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute yule coefficent — binary.yule","title":"Compute yule coefficent — binary.yule","text":"Compute yule coefficent","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute yule coefficent — binary.yule","text":"","code":"binary.yule(overlap, mat)"},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute yule coefficent — binary.yule","text":"overlap overlap matrixx mat gam","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute yule coefficent — binary.yule","text":"yule coefficent","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — effectSize","title":"Compute weight overlap stats — effectSize","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — effectSize","text":"","code":"effectSize(obs, exp)"},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — effectSize","text":"obs observed overlap exp expected overlap","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — effectSize","text":"effect size","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute FDR — estimateFDR2","title":"Compute FDR — estimateFDR2","text":"Compute FDR","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute FDR — estimateFDR2","text":"","code":"estimateFDR2(obs, exp, nSim, maxFDR = 0.25)"},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute FDR — estimateFDR2","text":"obs observed values exp expected values aka null model nSim weight matrix maxFDR maxFDR keep","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute FDR — estimateFDR2","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute pairwise p-value — estimate_p_val","title":"Compute pairwise p-value — estimate_p_val","text":"Compute pairwise p-value","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute pairwise p-value — estimate_p_val","text":"","code":"estimate_p_val(robs_co, obs.co, gene1, gene2)"},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute pairwise p-value — estimate_p_val","text":"robs_co observed values obs.co expected values aka null model gene1 weight matrix gene2 maxFDR keep","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute pairwise p-value — estimate_p_val","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute pairwise p-value — estimate_pairwise_p","title":"Compute pairwise p-value — estimate_pairwise_p","text":"Compute pairwise p-value","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute pairwise p-value — estimate_pairwise_p","text":"","code":"estimate_pairwise_p(obs, exp, results, nSim)"},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute pairwise p-value — estimate_pairwise_p","text":"obs observed values exp expected values aka null model results weight matrix nSim maxFDR keep","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute pairwise p-value — estimate_pairwise_p","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter maf function — filter_maf_column","title":"Filter maf function — filter_maf_column","text":"filter_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter maf function — filter_maf_column","text":"","code":"filter_maf_column(maf, values, column, inclusive = TRUE, fixed = TRUE, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter maf function — filter_maf_column","text":"maf maf dataframe values list containing elements filter column column maf file filter inclusive boolena include exclude dataframe values list provided fixed grep argument specify grep use argumnet string ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter maf function — filter_maf_column","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_complex.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values — filter_maf_complex","title":"This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values — filter_maf_complex","text":"function filters MAF dataframe retaining rows combination values compatible values","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_complex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values — filter_maf_complex","text":"","code":"filter_maf_complex(maf, values, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_gene.name.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_gene.name","title":"This function filters a MAF dataframe by sample id — filter_maf_gene.name","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_gene.name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_gene.name","text":"","code":"filter_maf_gene.name(maf, genes, gene.col = \"Hugo_Symbol\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"filter_maf_ignore() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"","code":"filter_maf_ignore(maf, schema = TCGA_maf_schema, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"filter_maf_missense() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"","code":"filter_maf_missense(maf, schema = TCGA_maf_schema, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutation.type.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_mutation.type","title":"This function filters a MAF dataframe by sample id — filter_maf_mutation.type","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutation.type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_mutation.type","text":"","code":"filter_maf_mutation.type( maf, variants, variant.col = \"Variant_Classification\", ... )"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutations.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_mutations","title":"This function filters a MAF dataframe by sample id — filter_maf_mutations","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_mutations","text":"","code":"filter_maf_mutations( maf, values, maf.col = c(\"Hugo_Symbol\", \"HGVSp_Short\"), values.col = maf.col, ... )"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_sample.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_sample","title":"This function filters a MAF dataframe by sample id — filter_maf_sample","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_sample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_sample","text":"","code":"filter_maf_sample(maf, samples, sample.col = \"Tumor_Sample_Barcode\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_schema","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"filter_maf_schema() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"","code":"filter_maf_schema(maf, schema = TCGA_maf_schema, column, values, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example column column maf file filter values list containing elements file ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"filter_maf_truncating() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"","code":"filter_maf_truncating(maf, schema = TCGA_maf_schema, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate S matrix — generateS","title":"Generate S matrix — generateS","text":"Generate S matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate S matrix — generateS","text":"","code":"generateS(gam, sample.weights, upperBound = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate S matrix — generateS","text":"gam gam genes*samples sample.weights samples weights upperBound clip values greater 1 keep bounded 0 1","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate S matrix — generateS","text":"S S matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the weight matrix taking sample covariate — generateW_block","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"Generating weight matrix taking sample covariate","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"","code":"generateW_block(al, lambda, tao)"},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"al altearting landscape onject lambda penalty factor parameter tao fold change paramenter","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"Weight matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the weight matrix — generateW_mean_tmb","title":"Generating the weight matrix — generateW_mean_tmb","text":"Generating weight matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the weight matrix — generateW_mean_tmb","text":"","code":"generateW_mean_tmb( tmb, mean_tmb, ngenes, lambda = 0.3, tao = 1, discrete = TRUE )"},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the weight matrix — generateW_mean_tmb","text":"tmb TMB dataframe mean_tmb TMB dataframe ngenes Number genes lambda 0.1 weight factor tao 1 Fold change factor discrete True discrete weights","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the weight matrix — generateW_mean_tmb","text":"weight matrix (.e vector matrix)","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":null,"dir":"Reference","previous_headings":"","what":"Get sample/alteration blocks — get.blocks","title":"Get sample/alteration blocks — get.blocks","text":"Get sample/alteration blocks","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get sample/alteration blocks — get.blocks","text":"","code":"get.blocks(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get sample/alteration blocks — get.blocks","text":"al alteration landscape","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get sample/alteration blocks — get.blocks","text":"Classification samples alterations blocks.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — interaction.table","title":"Compute weight overlap stats — interaction.table","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — interaction.table","text":"","code":"interaction.table( al, als, obs, wobs, r.obs = NULL, r.wobs = NULL, null, maxFDR = 0.2, n.cores = 1, estimate_pairwise = FALSE, n.permut = 1000 )"},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — interaction.table","text":"al alteration matrix als alteration matrix stats object obs observed overlap wobs weighted observed overlap r.obs random observed overlap r.wobs random weighted observed overlap null null model maxFDR maxFDR cutoff n.cores number cores estimate_pairwise Compute pairwise n.permut number permutation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — interaction.table","text":"table results","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_maf.html","id":null,"dir":"Reference","previous_headings":"","what":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","title":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","text":"MAF file LUAD TCGA","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_maf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","text":"","code":"data(luad_maf)"},{"path":"https://csogroup.github.io/SelectSim/reference/luad_maf.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","text":"dataframe","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","title":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","text":"Result LUAD generated selectX selectX run done min.freq=10.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","text":"","code":"data(luad_result)"},{"path":"https://csogroup.github.io/SelectSim/reference/luad_result.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","text":"dataframe","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_run_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","title":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","text":"dataset containing genome alteration matrix tumor mutation burden along sample,alteration annotation list object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_run_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","text":"","code":"data(luad_run_data)"},{"path":"https://csogroup.github.io/SelectSim/reference/luad_run_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","text":"list object GAMs TMBs along sample & alteration annotations.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate gam from the maf file — maf2gam","title":"Generate gam from the maf file — maf2gam","text":"maf2gam() takes maf file converts gam","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate gam from the maf file — maf2gam","text":"","code":"maf2gam( maf, sample.col = \"Tumor_Sample_Barcode\", gene.col = \"Hugo_Symbol\", value.var = \"HGVSp_Short\", samples = NULL, genes = NULL, fun.aggregate = length, binarize = TRUE, fill = NA, ... )"},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate gam from the maf file — maf2gam","text":"maf maf dataframe sample.col list containing elements filter gene.col column maf file filter value.var column maf file filter samples column maf file filter genes column maf file filter fun.aggregate column maf file filter binarize boolena include exclude dataframe values list provided fill grep argument specify grep use argumnet string ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate gam from the maf file — maf2gam","text":"filtered_maf GAM matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/mutation_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Mutation list object — mutation_type","title":"Mutation list object — mutation_type","text":"Mutation list object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/mutation_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mutation list object — mutation_type","text":"","code":"mutation_type"},{"path":"https://csogroup.github.io/SelectSim/reference/mutation_type.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Mutation list object — mutation_type","text":"object class list length 3.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an AL object — new.AL.general","title":"Create an AL object — new.AL.general","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an AL object — new.AL.general","text":"","code":"new.AL.general( am, feat.covariates = NULL, sample.covariates = NULL, min.freq, verbose = FALSE )"},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an AL object — new.AL.general","text":"binary alteration matrix row features column samples. feat.covariates gene/feature covariate. sample.covariates sample covariate. min.freq minimum frequency genes mutated. verbose print time steps.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an AL object — new.AL.general","text":"Alteration Landscape (AL) object gam.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration landscape object — new.ALS","title":"Create an alteration landscape object — new.ALS","text":"Create alteration landscape object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration landscape object — new.ALS","text":"","code":"new.ALS(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration landscape object — new.ALS","text":"al alteration landscape","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration landscape object — new.ALS","text":"AlS object.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration matrix stats object — new.AMS","title":"Create an alteration matrix stats object — new.AMS","text":"Create alteration matrix stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration matrix stats object — new.AMS","text":"","code":"new.AMS(am)"},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration matrix stats object — new.AMS","text":"alteration matrix stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration matrix stats object — new.AMS","text":"AMS object.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the null_simulation matrix — null_model_parallel","title":"Generating the null_simulation matrix — null_model_parallel","text":"Generating null_simulation matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the null_simulation matrix — null_model_parallel","text":"","code":"null_model_parallel(al, temp_mat, W, n.cores = 1, n.permut)"},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the null_simulation matrix — null_model_parallel","text":"al Alteration landscape object temp_mat template matrixes W weight matrix n.cores Number cores n.permut Number simulation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the null_simulation matrix — null_model_parallel","text":"Template matrix list object Ordering genes impacts results residual subraction correct.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the null_simulation matrix — null_model_parallel_debug","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"Generating null_simulation matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"","code":"null_model_parallel_debug(al, temp_mat, W, n.cores = 1, n.permut)"},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"al Alteration landscape object temp_mat template matrixes W weight matrix n.cores Number cores n.permut Number simulation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"Template matrix list object Ordering genes impacts results residual subraction correct.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an AL object — obs_exp_scatter","title":"Create an AL object — obs_exp_scatter","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an AL object — obs_exp_scatter","text":"","code":"obs_exp_scatter(result, title)"},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an AL object — obs_exp_scatter","text":"result result table selectX obj$result title title plot","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an AL object — obs_exp_scatter","text":"ggplot2 object observed vs random overlap plot.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"OncoKB v3.9 cancer genes — oncokb_genes","title":"OncoKB v3.9 cancer genes — oncokb_genes","text":"cancer genes list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OncoKB v3.9 cancer genes — oncokb_genes","text":"","code":"data(oncokb_genes)"},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_genes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"OncoKB v3.9 cancer genes — oncokb_genes","text":"list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_truncating_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","title":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","text":"cancer genes list consider truncating mutations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_truncating_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","text":"","code":"data(oncokb_truncating_genes)"},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_truncating_genes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","text":"list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract the backgroun distribution — overlap_pair_extract","title":"Extract the backgroun distribution — overlap_pair_extract","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract the backgroun distribution — overlap_pair_extract","text":"","code":"overlap_pair_extract(gene1, gene2, obj)"},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract the backgroun distribution — overlap_pair_extract","text":"gene1 gene1 gene2 gene2 obj selectX obj","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract the backgroun distribution — overlap_pair_extract","text":"backgorund distribution vector.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"","code":"r.am.pairwise.alteration.overlap(null, n.permut, n.cores = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"null null model n.permut number permutation steps n.cores number cores","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — r.effectSize","title":"Compute weight overlap stats — r.effectSize","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — r.effectSize","text":"","code":"r.effectSize(null_overlap, mean_mat, n.permut = 1000, n.cores = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — r.effectSize","text":"null_overlap null model overlap mean_mat mean effect size vector n.permut number permutation steps n.cores number cores","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — r.effectSize","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":null,"dir":"Reference","previous_headings":"","what":"Removing the Outliers — retrieveOutliers","title":"Removing the Outliers — retrieveOutliers","text":"Removing Outliers","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removing the Outliers — retrieveOutliers","text":"","code":"retrieveOutliers(obj, nSim = 1000)"},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removing the Outliers — retrieveOutliers","text":"obj selectX object nSim Number simulation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Removing the Outliers — retrieveOutliers","text":"outliers","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a pairs background plot — ridge_plot_ed","title":"Generate a pairs background plot — ridge_plot_ed","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a pairs background plot — ridge_plot_ed","text":"","code":"ridge_plot_ed(result_df, obj)"},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a pairs background plot — ridge_plot_ed","text":"result_df result table selectX obj$result obj selectX obj","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a pairs background plot — ridge_plot_ed","text":"ggplot2 object observed vs random overlap plot.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"","code":"ridge_plot_ed_compare(result_df, obj1, obj2, name1, name2)"},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"result_df common result table selectX obj$result dataset1_w_overlap dataset2_w_overlap columns obj1 selectX obj dataset1 obj2 selectX obj dataset2 name1 dataset1 name name2 dataset2 name","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"ggplot2 object observed vs random overlap plot.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":null,"dir":"Reference","previous_headings":"","what":"SelectX main function to create alteration object with background model — selectX","title":"SelectX main function to create alteration object with background model — selectX","text":"selectX() takes list object consist genome alteration matrix tumor mutation burden.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SelectX main function to create alteration object with background model — selectX","text":"","code":"selectX( M, sample.class, alteration.class, n.cores = 1, min.freq = 10, n.permut = 1000, lambda = 0.3, tao = 1, save.object = FALSE, folder = \"./\", verbose = TRUE, estimate_pairwise = FALSE, maxFDR = 0.25, seed = 42 )"},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SelectX main function to create alteration object with background model — selectX","text":"M list data object consist gams tmbs. sample.class sample covariates named list. alteration.class alteration covariates named list. n.cores cores. min.freq number samples features atleast mutated . n.permut number simulations. lambda lambda parameter. tao tao parameter. save.object store SelectX object. folder folder path store results. verbose print time steps. estimate_pairwise Compute pairwise p-value maxFDR FDR value seed random seed","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"SelectX main function to create alteration object with background model — selectX","text":"result SelectX object background model info along result table","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":null,"dir":"Reference","previous_headings":"","what":"SelectX main function to create alteration object with background model — selectX_debug","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"selectX() takes list object consist genome alteration matrix tumor mutation burden.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"","code":"selectX_debug( M, sample.class, alteration.class, n.cores = 1, min.freq = 10, n.permut = 1000, lambda = 0.3, tao = 1, save.object = FALSE, folder = \"./\", verbose = TRUE, estimate_pairwise = FALSE, maxFDR = 0.25, seed = 42 )"},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"M list data object consist gams tmbs. sample.class sample covariates named list. alteration.class alteration covariates named list. n.cores cores. min.freq number samples features atleast mutated . n.permut number simulations. lambda lambda parameter. tao tao parameter. save.object store SelectX object. folder folder path store results. verbose print time steps. estimate_pairwise Compute pairwise p-value maxFDR FDR value seed random seed","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"result SelectX object background model info along result table","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary functions for MAF file — stat_maf_column","title":"Summary functions for MAF file — stat_maf_column","text":"stat_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary functions for MAF file — stat_maf_column","text":"","code":"stat_maf_column(maf, column, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary functions for MAF file — stat_maf_column","text":"maf maf dataframe column schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary functions for MAF file — stat_maf_column","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary functions for MAF file — stat_maf_gene","title":"Summary functions for MAF file — stat_maf_gene","text":"stat_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary functions for MAF file — stat_maf_gene","text":"","code":"stat_maf_gene(maf, column = \"Hugo_Symbol\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary functions for MAF file — stat_maf_gene","text":"maf maf dataframe column schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary functions for MAF file — stat_maf_gene","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary functions for MAF file — stat_maf_sample","title":"Summary functions for MAF file — stat_maf_sample","text":"stat_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary functions for MAF file — stat_maf_sample","text":"","code":"stat_maf_sample(maf, column = \"Tumor_Sample_Barcode\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary functions for MAF file — stat_maf_sample","text":"maf maf dataframe column schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary functions for MAF file — stat_maf_sample","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the template matrix — templeate.obj.gen","title":"Generating the template matrix — templeate.obj.gen","text":"Computing expected mutation background matrix using simulation done.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the template matrix — templeate.obj.gen","text":"","code":"templeate.obj.gen(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the template matrix — templeate.obj.gen","text":"al Alteration landscape object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the template matrix — templeate.obj.gen","text":"Template matrix list object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/variant_catalogue.html","id":null,"dir":"Reference","previous_headings":"","what":"OncoKB v3.9 cancer genes — variant_catalogue","title":"OncoKB v3.9 cancer genes — variant_catalogue","text":"dataframe cancer genes missense mutation annotations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/variant_catalogue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OncoKB v3.9 cancer genes — variant_catalogue","text":"","code":"data(variant_catalogue)"},{"path":"https://csogroup.github.io/SelectSim/reference/variant_catalogue.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"OncoKB v3.9 cancer genes — variant_catalogue","text":"dataframe","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"","code":"w.r.am.pairwise.alteration.overlap(null, W, n.permut, n.cores = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"null null model W weight matrix n.permut number permutation steps n.cores number cores","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"overlap weight overlap pairs","code":""},{"path":[]}]
+[{"path":"https://csogroup.github.io/SelectSim/INSTALLATION.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"NA","text":"can install development version SelectSim GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/INSTALLATION.html","id":"installation-with-micromamba-enviorment","dir":"","previous_headings":"","what":"Installation with micromamba enviorment","title":"NA","text":"micromamba tiny version mamba package manager (Like Conda). Refer website ’s installation guide. Steps follow installing micromamba terminal: micromamba create -n r_env r-essentials r-base micromamba activate r_env micromamba install conda-forge::r-devtools micromamba install conda-forge::armadillo micromamba install conda-forge::r-rcppparallel micromamba install conda-forge::r-rfast run R install SelectSim R package follows Alternative way install provided enviorment.yml file. micromamba create -f env.yml micromamba activate r_env - run R install SelectSim R package follows","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE) # install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 SelectSim authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Data_processing","text":"can install development version SelectSim GitHub : details installation refer INSTALLATION","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Data_processing","text":"process LUAD MAF dataset TCGA provided package. also use oncokb v3.9 cancer genes mutations filter maf create gam provided pacakge. NOTE: example prcoess MAF file. know prcossed MAF file run_data object, please refer SelectSim_analysis repository. Let print number lines number samples Let create table schema mutations conisder columns defined maf file Number samples maf file Filter maf file include oncokb cancer genes","code":"library(SelectSim) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(tictoc) ## Load the data provided with the package data(luad_maf, package = \"SelectSim\") data(oncokb_genes, package = \"SelectSim\") data(oncokb_truncating_genes, package = \"SelectSim\") data(variant_catalogue, package = \"SelectSim\") # Check the MAF dim(luad_maf) #> [1] 220734 8 input_maf <- luad_maf print(paste('##### Number of lines ####',nrow(input_maf),sep=\"->\")) #> [1] \"##### Number of lines ####->220734\" genes_to_consider = oncokb_genes print(paste('##### Number of genes ####',length(genes_to_consider),sep=\"->\")) #> [1] \"##### Number of genes ####->396\" mutation_type = list( 'ignore' = c(\"Silent\",\"Intron\",\"RNA\",\"3'UTR\",\"5'UTR\",\"5'Flank\",\"3'Flank\",\"IGR\"), 'truncating'= c('Frame_Shift_Del','Frame_Shift_Ins','In_Frame_Del','In_Frame_Ins','Nonsense_Mutation','Nonstop_Mutation','Splice_Region','Splice_Site','Translation_Start_Site'), 'missense' = c('Missense_Mutation') ) custom_maf_schema = list( 'name' = 'custom_maf', 'column' = list( 'gene' = 'Hugo_Symbol' , 'gene.name' = 'Hugo_Symbol' , 'sample' = 'sample' , 'sample.name' = 'sample' , 'mutation.type' = 'Variant_Classification' , 'mutation' = 'HGVSp_Short' ), 'mutation.type' = mutation_type ) mut_samples = unique(input_maf[, custom_maf_schema$column$sample]) print(paste('##### Number of samples ####',length(mut_samples),sep=\"->\")) #> [1] \"##### Number of samples ####->502\" maf_genes = filter_maf_gene.name(input_maf, genes = genes_to_consider, gene.col = custom_maf_schema$column$gene) print(paste('##### Number of lines ####',nrow(maf_genes),sep=\"->\")) #> [1] \"##### Number of lines ####->6708\""},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"genrating-the-gams","dir":"Articles","previous_headings":"Example","what":"Genrating the GAMs","title":"Data_processing","text":"generate GAM consider genes consider truncating mutations. also create TMB dataframe takes truncating mutation genes consideration. generate GAM genes hotspot mutations oncokb v3.9. also create TMB dataframe takes Missense mutation genes consideration.","code":"# Creating Truncating GAM tic('##### Creating Truncating GAM ####') maf_trunc = filter_maf_truncating(maf_genes,genes=oncokb_truncating_genes, custom_maf_schema) input_maf_trunc<-filter_maf_truncating(input_maf, custom_maf_schema) truncating_tmb <- data.frame('sample'=mut_samples,'mutation'=rep(0,length(mut_samples))) rownames(truncating_tmb)<-mut_samples temp <- input_maf_trunc %>% count(sample) rownames(temp)<-temp$sample truncating_tmb[intersect(truncating_tmb$sample,temp$sample),]$mutation <-temp[intersect(truncating_tmb$sample,temp$sample),'n'] tcga_truc_gam = maf2gam(maf_trunc, sample.col = custom_maf_schema$column$sample, gene.col = custom_maf_schema$column$gene, value.var = 'Variant_Classification', samples = mut_samples, genes = genes_to_consider, fun.aggregate = length, binarize=TRUE, fill=0) truncating_data <- list('gam'=tcga_truc_gam, 'tmb'=truncating_tmb) toc() #> ##### Creating Truncating GAM ####: 0.216 sec elapsed # Creating Missense GAM tic('##### Creating Missense GAM ####') maf_valid = filter_maf_schema(input_maf, schema = custom_maf_schema, column = 'mutation.type', values = custom_maf_schema[['mutation.type']][['ignore']], inclusive = FALSE) missense_maf<-filter_maf_mutation.type(input_maf, variants = 'Missense_Mutation', variant.col = custom_maf_schema$column$mutation.type) missense_tmb <- data.frame('sample'=mut_samples,'mutation'=rep(0,length(mut_samples))) rownames(missense_tmb)<-mut_samples temp <- missense_maf %>% count(sample) rownames(temp)<-temp$sample missense_tmb[intersect(missense_tmb$sample,temp$sample),]$mutation <-temp[intersect(missense_tmb$sample,temp$sample),'n'] t_m = substr(maf_valid[[custom_maf_schema$column$mutation]],3,1000) t_m1 = gsub('[A-Z]*$', '', t_m) maf_valid$HGVSp_Short_fixed = t_m1 maf_hotspot = filter_maf_mutations(maf_valid, variant_catalogue, maf.col = c(custom_maf_schema$column$gene, 'HGVSp_Short_fixed'), values.col = c('gene', 'mut')) missense_tcga_gam = maf2gam(maf_hotspot, sample.col = custom_maf_schema$column$sample, gene.col = custom_maf_schema$column$gene, value.var = 'Variant_Classification', samples = mut_samples, genes = genes_to_consider, fun.aggregate = length, binarize=TRUE, fill=0) missesne_data <- list('gam'=missense_tcga_gam, 'tmb'=missense_tmb) toc() #> ##### Creating Missense GAM ####: 1.713 sec elapsed"},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"genrating-the-run_object-to-run-selectx","dir":"Articles","previous_headings":"Example","what":"Genrating the run_object to run SelectX","title":"Data_processing","text":"M: list object GAMs presence absence matrix alterations tmb: list object tumor mutation burden data frame column names () sample mutationn sample.class named vector sample annotations alteration.class named vector alteration annotations Save run_data check introduction vignette see run selectX discover EDs.","code":"gene_to_take <- colnames(missesne_data$gam) order <- rownames(missesne_data$gam) data <-list('M'=list('missense'=t(missesne_data$gam[order,gene_to_take]), 'truncating'=t(truncating_data$gam[rownames(missesne_data$gam[order,]),gene_to_take])), 'tmb'=list('missense'=missesne_data$tmb[order,], 'truncating'=truncating_data$tmb[order,])) alteration_covariates <- rep('MUT',ncol(missesne_data$gam[order,gene_to_take])) names(alteration_covariates)<-colnames(missesne_data$gam[order,gene_to_take]) sample_covariates<-rep('LUAD',length(order)) names(sample_covariates)<-order run_data <- list('M'=data,'sample.class' = sample_covariates,'alteration.class' = alteration_covariates) str(run_data) #> List of 3 #> $ M :List of 2 #> ..$ M :List of 2 #> .. ..$ missense : num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ATM\" \"BRAF\" \"CDKN2A\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. ..$ truncating: num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ATM\" \"BRAF\" \"CDKN2A\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> ..$ tmb:List of 2 #> .. ..$ missense :'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 163 253 270 1328 100 ... #> .. ..$ truncating:'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 24 45 40 206 17 18 73 31 176 108 ... #> $ sample.class : Named chr [1:502] \"LUAD\" \"LUAD\" \"LUAD\" \"LUAD\" ... #> ..- attr(*, \"names\")= chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> $ alteration.class: Named chr [1:396] \"MUT\" \"MUT\" \"MUT\" \"MUT\" ... #> ..- attr(*, \"names\")= chr [1:396] \"AKT1\" \"ATM\" \"BRAF\" \"CDKN2A\" ..."},{"path":"https://csogroup.github.io/SelectSim/articles/data_processing.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"Data_processing","text":"","code":"# Print the sessionInfo sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-conda-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /mnt/ndata/arvind/envs/R_4/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> time zone: Europe/Zurich #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] tictoc_1.2 dplyr_1.1.4 SelectSim_0.0.1.3 #> #> loaded via a namespace (and not attached): #> [1] gtable_0.3.4 xfun_0.41 bslib_0.6.1 ggplot2_3.4.4 #> [5] rstatix_0.7.2 lattice_0.22-5 vctrs_0.6.5 tools_4.3.2 #> [9] generics_0.1.3 parallel_4.3.2 tibble_3.2.1 fansi_1.0.6 #> [13] pkgconfig_2.0.3 Matrix_1.6-5 desc_1.4.3 ggridges_0.5.5 #> [17] rngtools_1.5.2 RcppParallel_5.1.6 lifecycle_1.0.4 compiler_4.3.2 #> [21] stringr_1.5.1 textshaping_0.3.7 munsell_0.5.0 codetools_0.2-19 #> [25] carData_3.0-5 htmltools_0.5.7 sass_0.4.8 yaml_2.3.8 #> [29] pillar_1.9.0 pkgdown_2.0.7 car_3.1-2 ggpubr_0.6.0 #> [33] jquerylib_0.1.4 tidyr_1.3.0 cachem_1.0.8 doRNG_1.8.6 #> [37] iterators_1.0.14 abind_1.4-5 foreach_1.5.2 tidyselect_1.2.0 #> [41] digest_0.6.34 stringi_1.8.3 reshape2_1.4.4 purrr_1.0.2 #> [45] fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0 cli_3.6.2 #> [49] magrittr_2.0.3 Rfast_2.1.0 utf8_1.2.4 broom_1.0.5 #> [53] scales_1.3.0 backports_1.4.1 RcppZiggurat_0.1.6 rmarkdown_2.25 #> [57] ggsignif_0.6.4 ragg_1.2.7 memoise_2.0.1 evaluate_0.23 #> [61] knitr_1.45 doParallel_1.0.17 rlang_1.1.3 Rcpp_1.0.12 #> [65] glue_1.7.0 jsonlite_1.8.8 R6_2.5.1 plyr_1.8.9 #> [69] systemfonts_1.0.5 fs_1.6.3"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"can install development version SelectSim GitHub : details installation refer INSTALLATION","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"run SelectSim algorithm processed LUAD dataset TCGA provided package. Note: example running processed data. Check vignette process data create run_data object needed input SelectSim algorithm.","code":"library(SelectSim) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union ## Load the data provided with the package data(luad_run_data, package = \"SelectSim\")"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"data-description-format","dir":"Articles","previous_headings":"Example","what":"Data Description & Format","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"M: list object GAMs presence absence matrix alterations tmb: list object tumor mutation burden data frame column names () sample mutationn sample.class named vector sample annotations alteration.class named vector alteration annotations","code":"# Check the data strucutre str(luad_run_data) #> List of 3 #> $ M :List of 2 #> ..$ M :List of 2 #> .. ..$ missense : num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ALK\" \"APC\" \"AR\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. ..$ truncating: num [1:396, 1:502] 0 0 0 0 0 0 0 0 0 0 ... #> .. .. ..- attr(*, \"dimnames\")=List of 2 #> .. .. .. ..$ : chr [1:396] \"AKT1\" \"ALK\" \"APC\" \"AR\" ... #> .. .. .. ..$ : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> ..$ tmb:List of 2 #> .. ..$ missense :'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 163 253 270 1328 100 ... #> .. ..$ truncating:'data.frame': 502 obs. of 2 variables: #> .. .. ..$ sample : chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> .. .. ..$ mutation: num [1:502] 24 45 40 206 17 18 73 31 176 108 ... #> $ sample.class : Named chr [1:502] \"LUAD\" \"LUAD\" \"LUAD\" \"LUAD\" ... #> ..- attr(*, \"names\")= chr [1:502] \"TCGA-05-4244-01\" \"TCGA-05-4249-01\" \"TCGA-05-4250-01\" \"TCGA-05-4382-01\" ... #> $ alteration.class: Named chr [1:396] \"MUT\" \"MUT\" \"MUT\" \"MUT\" ... #> ..- attr(*, \"names\")= chr [1:396] \"AKT1\" \"ALK\" \"APC\" \"AR\" ..."},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"running-selectx","dir":"Articles","previous_headings":"Example","what":"Running SelectX","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"use function selectX() generates background model results. M: list object GAMs & TMB sample.class: named vector samples covariates alteration.class: named vector alteration covariates min.freq: Number samples gene mutated atleast n.permut: Number simulation lambda: Penalty factor used computing penalty vector tao: Fold chnage factor used computing penalty vector maxFDR: FDR rate call significnat results function returns list object contains background model results.","code":"result_obj<- selectX( M = luad_run_data$M, sample.class = luad_run_data$sample.class, alteration.class = luad_run_data$alteration.class, n.cores = 1, min.freq = 10, n.permut = 1000, lambda = 0.3, tao = 1, save.object = FALSE, verbose = FALSE, estimate_pairwise = FALSE, maxFDR = 0.25) #> Total Time: 4.449 sec elapsed"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"intrepreting-the-results","dir":"Articles","previous_headings":"Example","what":"Intrepreting the results","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"Lets look results","code":"head(result_obj$result[,1:10],n=5) #> SFE_1 SFE_2 name support_1 support_2 freq_1 freq_2 #> KRAS - TP53 KRAS TP53 KRAS - TP53 154 221 0.30677291 0.4402390 #> EGFR - KRAS EGFR KRAS EGFR - KRAS 57 154 0.11354582 0.3067729 #> STK11 - TP53 STK11 TP53 STK11 - TP53 59 221 0.11752988 0.4402390 #> BRAF - KRAS BRAF KRAS BRAF - KRAS 35 154 0.06972112 0.3067729 #> KRAS - STK11 KRAS STK11 KRAS - STK11 154 59 0.30677291 0.1175299 #> overlap w_overlap max_overlap #> KRAS - TP53 49 35.8760174 154 #> EGFR - KRAS 0 0.0000000 57 #> STK11 - TP53 13 9.5456386 59 #> BRAF - KRAS 2 0.9821429 35 #> KRAS - STK11 28 25.9230769 59"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"filtering-significant-hits","dir":"Articles","previous_headings":"Example > Intrepreting the results","what":"Filtering significant hits","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"","code":"# Filtering significant hits and counting EDs result_obj$result %>% filter(nFDR2<=0.25) %>% head(n=2) #> SFE_1 SFE_2 name support_1 support_2 freq_1 freq_2 #> KRAS - TP53 KRAS TP53 KRAS - TP53 154 221 0.3067729 0.4402390 #> EGFR - KRAS EGFR KRAS EGFR - KRAS 57 154 0.1135458 0.3067729 #> overlap w_overlap max_overlap freq_overlap r_overlap w_r_overlap #> KRAS - TP53 49 35.87602 154 0.3181818 99.02908 58.69631 #> EGFR - KRAS 0 0.00000 57 0.0000000 31.22148 16.85637 #> wES wFDR nES mean_r_nES nFDR cum_freq nFDR2 type FDR #> KRAS - TP53 -16.13638 0 -14.18270 -1.953683 0 375 0 ME TRUE #> EGFR - KRAS -11.91926 0 -10.72977 -1.189488 0 211 0 ME TRUE result_obj$result %>% filter(nFDR2<=0.25) %>% count(type) #> type n #> 1 CO 13 #> 2 ME 30"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"plotting-a-scatter-plot-of-co-mutation","dir":"Articles","previous_headings":"Example > Intrepreting the results","what":"Plotting a scatter plot of co-mutation","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"","code":"# Filtering significant hits and plotting options(repr.plot.width = 7, repr.plot.height = 7) obs_exp_scatter(result = result_obj$result,title = 'TCGA LUAD')"},{"path":"https://csogroup.github.io/SelectSim/articles/introduction.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"Introduction to finding evolutionary dependencies in cancer data using SelectSim algorithm","text":"","code":"# Print the sessionInfo sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-conda-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /mnt/ndata/arvind/envs/R_4/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> time zone: Europe/Zurich #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] dplyr_1.1.4 SelectSim_0.0.1.3 #> #> loaded via a namespace (and not attached): #> [1] gtable_0.3.4 xfun_0.41 bslib_0.6.1 ggplot2_3.4.4 #> [5] rstatix_0.7.2 lattice_0.22-5 vctrs_0.6.5 tools_4.3.2 #> [9] generics_0.1.3 parallel_4.3.2 tibble_3.2.1 fansi_1.0.6 #> [13] highr_0.10 pkgconfig_2.0.3 Matrix_1.6-5 desc_1.4.3 #> [17] ggridges_0.5.5 rngtools_1.5.2 RcppParallel_5.1.6 lifecycle_1.0.4 #> [21] farver_2.1.1 compiler_4.3.2 stringr_1.5.1 tictoc_1.2 #> [25] textshaping_0.3.7 munsell_0.5.0 codetools_0.2-19 carData_3.0-5 #> [29] htmltools_0.5.7 sass_0.4.8 yaml_2.3.8 pillar_1.9.0 #> [33] pkgdown_2.0.7 car_3.1-2 ggpubr_0.6.0 jquerylib_0.1.4 #> [37] tidyr_1.3.0 cachem_1.0.8 doRNG_1.8.6 iterators_1.0.14 #> [41] abind_1.4-5 foreach_1.5.2 tidyselect_1.2.0 digest_0.6.34 #> [45] stringi_1.8.3 reshape2_1.4.4 purrr_1.0.2 fastmap_1.1.1 #> [49] grid_4.3.2 colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3 #> [53] Rfast_2.1.0 utf8_1.2.4 broom_1.0.5 withr_3.0.0 #> [57] scales_1.3.0 backports_1.4.1 RcppZiggurat_0.1.6 rmarkdown_2.25 #> [61] ggsignif_0.6.4 ragg_1.2.7 memoise_2.0.1 evaluate_0.23 #> [65] knitr_1.45 doParallel_1.0.17 rlang_1.1.3 Rcpp_1.0.12 #> [69] glue_1.7.0 jsonlite_1.8.8 R6_2.5.1 plyr_1.8.9 #> [73] systemfonts_1.0.5 fs_1.6.3"},{"path":"https://csogroup.github.io/SelectSim/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Arvind Iyer. Author, maintainer. Marco Mina. Author. Giovanni Ciriello. Author.","code":""},{"path":"https://csogroup.github.io/SelectSim/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Iyer , Mina M, Ciriello G (2024). SelectSim: Selected Events Linked Evolutionary Conditions across human Tumors. R package version 0.0.1.3, https://csogroup.github.io/SelectSim/.","code":"@Manual{, title = {SelectSim: Selected Events Linked by Evolutionary Conditions across human Tumors}, author = {Arvind Iyer and Marco Mina and Giovanni Ciriello}, year = {2024}, note = {R package version 0.0.1.3}, url = {https://csogroup.github.io/SelectSim/}, }"},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"selectsim-","dir":"","previous_headings":"","what":"Selected Events Linked by Evolutionary Conditions across human Tumors","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"goal SelectSim package implement methodology infer inter-dependencies functional alterations cancer. SelectSim estimates expected number mutations given gene given sample mutation frequency gene, f(g), tumor mutation burden (TMB) sample, μ(t). values can estimated within specific mutation tumor subsets, account heterogeneous tumor types, tissue specificities, distinct mutational processes SelectSim Method","code":""},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"can install development version SelectSim GitHub : details installation refer INSTALLATION","code":"# install.packages(\"devtools\") devtools::install_github(\"CSOgroup/SelectSim\",dependencies = TRUE, build_vignettes = TRUE)"},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"Check Vignettes folder visit website","code":""},{"path":"https://csogroup.github.io/SelectSim/index.html","id":"who-do-i-talk-to","dir":"","previous_headings":"Example","what":"Who do I talk to?","title":"Selected Events Linked by Evolutionary Conditions across human Tumors","text":"bugs feature support using SelectSim, please use issue tracker. question related SelectSim, please contact Prof Giovanni Ciriello (giovanni.ciriello@unil.ch) Arvind Iyer (arvind.iyer@unil.ch).","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/GENIE_maf_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","title":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","text":"GENIE_maf_schema: GENIE_maf_schema: schema TCGA maf file process mutations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/GENIE_maf_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","text":"","code":"GENIE_maf_schema"},{"path":"https://csogroup.github.io/SelectSim/reference/GENIE_maf_schema.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations — GENIE_maf_schema","text":"object class list length 2.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/TCGA_maf_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","title":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","text":"TCGA_maf_schema: schema TCGA maf file process mutations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/TCGA_maf_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","text":"","code":"TCGA_maf_schema"},{"path":"https://csogroup.github.io/SelectSim/reference/TCGA_maf_schema.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"TCGA_maf_schema: schema for TCGA maf file to process the mutations — TCGA_maf_schema","text":"object class list length 3.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — add","title":"Compute weight overlap stats — add","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — add","text":"","code":"add(x)"},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — add","text":"x alteration matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/add.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — add","text":"average","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — al.pairwise.alteration.stats","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"","code":"al.pairwise.alteration.stats(al, als = NULL, do.blocks = FALSE)"},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"al alteration landscape object als alteration stats object .blocks blockwise comptutation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.pairwise.alteration.stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — al.pairwise.alteration.stats","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration stats object — al.stats","title":"Create an alteration stats object — al.stats","text":"Create alteration stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration stats object — al.stats","text":"","code":"al.stats(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration stats object — al.stats","text":"al alteration landscape object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/al.stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration stats object — al.stats","text":"als alteration landscape stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — am.pairwise.alteration.coverage","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"","code":"am.pairwise.alteration.coverage(overlap_M, M.stats, w_overlap_M)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"overlap_M overlap matrix M.stats matrix statis w_overlap_M weighted overlap matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.coverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — am.pairwise.alteration.coverage","text":"stats matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute overlap stats — am.pairwise.alteration.overlap","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"Compute overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"","code":"am.pairwise.alteration.overlap(am)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"alteration matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute overlap stats — am.pairwise.alteration.overlap","text":"overlap overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration matrix stats object — am.stats","title":"Create an alteration matrix stats object — am.stats","text":"Create alteration matrix stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration matrix stats object — am.stats","text":"","code":"am.stats(am)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration matrix stats object — am.stats","text":"alteration matrix stat object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration matrix stats object — am.stats","text":"AMS object basic stats matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"","code":"am.weight.pairwise.alteration.overlap(am, W)"},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"alteration matrix W weight matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/am.weight.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — am.weight.pairwise.alteration.overlap","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute yule coefficent — binary.yule","title":"Compute yule coefficent — binary.yule","text":"Compute yule coefficent","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute yule coefficent — binary.yule","text":"","code":"binary.yule(overlap, mat)"},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute yule coefficent — binary.yule","text":"overlap overlap matrixx mat gam","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/binary.yule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute yule coefficent — binary.yule","text":"yule coefficent","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — effectSize","title":"Compute weight overlap stats — effectSize","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — effectSize","text":"","code":"effectSize(obs, exp)"},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — effectSize","text":"obs observed overlap exp expected overlap","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/effectSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — effectSize","text":"effect size","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute FDR — estimateFDR2","title":"Compute FDR — estimateFDR2","text":"Compute FDR","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute FDR — estimateFDR2","text":"","code":"estimateFDR2(obs, exp, nSim, maxFDR = 0.25)"},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute FDR — estimateFDR2","text":"obs observed values exp expected values aka null model nSim weight matrix maxFDR maxFDR keep","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimateFDR2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute FDR — estimateFDR2","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute pairwise p-value — estimate_p_val","title":"Compute pairwise p-value — estimate_p_val","text":"Compute pairwise p-value","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute pairwise p-value — estimate_p_val","text":"","code":"estimate_p_val(robs_co, obs.co, gene1, gene2)"},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute pairwise p-value — estimate_p_val","text":"robs_co observed values obs.co expected values aka null model gene1 weight matrix gene2 maxFDR keep","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_p_val.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute pairwise p-value — estimate_p_val","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute pairwise p-value — estimate_pairwise_p","title":"Compute pairwise p-value — estimate_pairwise_p","text":"Compute pairwise p-value","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute pairwise p-value — estimate_pairwise_p","text":"","code":"estimate_pairwise_p(obs, exp, results, nSim)"},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute pairwise p-value — estimate_pairwise_p","text":"obs observed values exp expected values aka null model results weight matrix nSim maxFDR keep","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/estimate_pairwise_p.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute pairwise p-value — estimate_pairwise_p","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter maf function — filter_maf_column","title":"Filter maf function — filter_maf_column","text":"filter_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter maf function — filter_maf_column","text":"","code":"filter_maf_column(maf, values, column, inclusive = TRUE, fixed = TRUE, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter maf function — filter_maf_column","text":"maf maf dataframe values list containing elements filter column column maf file filter inclusive boolena include exclude dataframe values list provided fixed grep argument specify grep use argumnet string ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_column.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter maf function — filter_maf_column","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_complex.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values — filter_maf_complex","title":"This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values — filter_maf_complex","text":"function filters MAF dataframe retaining rows combination values compatible values","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_complex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values — filter_maf_complex","text":"","code":"filter_maf_complex(maf, values, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_gene.name.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_gene.name","title":"This function filters a MAF dataframe by sample id — filter_maf_gene.name","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_gene.name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_gene.name","text":"","code":"filter_maf_gene.name(maf, genes, gene.col = \"Hugo_Symbol\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"filter_maf_ignore() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"","code":"filter_maf_ignore(maf, schema = TCGA_maf_schema, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_ignore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by retaining (or discarding) ignore mutations — filter_maf_ignore","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"filter_maf_missense() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"","code":"filter_maf_missense(maf, schema = TCGA_maf_schema, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_missense.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by retaining (or discarding) missense mutations — filter_maf_missense","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutation.type.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_mutation.type","title":"This function filters a MAF dataframe by sample id — filter_maf_mutation.type","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutation.type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_mutation.type","text":"","code":"filter_maf_mutation.type( maf, variants, variant.col = \"Variant_Classification\", ... )"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutations.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_mutations","title":"This function filters a MAF dataframe by sample id — filter_maf_mutations","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_mutations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_mutations","text":"","code":"filter_maf_mutations( maf, values, maf.col = c(\"Hugo_Symbol\", \"HGVSp_Short\"), values.col = maf.col, ... )"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_sample.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_sample","title":"This function filters a MAF dataframe by sample id — filter_maf_sample","text":"function filters MAF dataframe sample id","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_sample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_sample","text":"","code":"filter_maf_sample(maf, samples, sample.col = \"Tumor_Sample_Barcode\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by sample id — filter_maf_schema","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"filter_maf_schema() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"","code":"filter_maf_schema(maf, schema = TCGA_maf_schema, column, values, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example column column maf file filter values list containing elements file ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by sample id — filter_maf_schema","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":null,"dir":"Reference","previous_headings":"","what":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"filter_maf_truncating() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"","code":"filter_maf_truncating(maf, schema = TCGA_maf_schema, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"maf maf dataframe schema schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/filter_maf_truncating.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function filters a MAF dataframe by retaining (or discarding) truncating mutations — filter_maf_truncating","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate S matrix — generateS","title":"Generate S matrix — generateS","text":"Generate S matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate S matrix — generateS","text":"","code":"generateS(gam, sample.weights, upperBound = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate S matrix — generateS","text":"gam gam genes*samples sample.weights samples weights upperBound clip values greater 1 keep bounded 0 1","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate S matrix — generateS","text":"S S matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the weight matrix taking sample covariate — generateW_block","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"Generating weight matrix taking sample covariate","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"","code":"generateW_block(al, lambda, tao)"},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"al altearting landscape onject lambda penalty factor parameter tao fold change paramenter","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_block.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the weight matrix taking sample covariate — generateW_block","text":"Weight matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the weight matrix — generateW_mean_tmb","title":"Generating the weight matrix — generateW_mean_tmb","text":"Generating weight matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the weight matrix — generateW_mean_tmb","text":"","code":"generateW_mean_tmb( tmb, mean_tmb, ngenes, lambda = 0.3, tao = 1, discrete = TRUE )"},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the weight matrix — generateW_mean_tmb","text":"tmb TMB dataframe mean_tmb TMB dataframe ngenes Number genes lambda 0.1 weight factor tao 1 Fold change factor discrete True discrete weights","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/generateW_mean_tmb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the weight matrix — generateW_mean_tmb","text":"weight matrix (.e vector matrix)","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":null,"dir":"Reference","previous_headings":"","what":"Get sample/alteration blocks — get.blocks","title":"Get sample/alteration blocks — get.blocks","text":"Get sample/alteration blocks","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get sample/alteration blocks — get.blocks","text":"","code":"get.blocks(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get sample/alteration blocks — get.blocks","text":"al alteration landscape","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/get.blocks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get sample/alteration blocks — get.blocks","text":"Classification samples alterations blocks.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — interaction.table","title":"Compute weight overlap stats — interaction.table","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — interaction.table","text":"","code":"interaction.table( al, als, obs, wobs, r.obs = NULL, r.wobs = NULL, null, maxFDR = 0.2, n.cores = 1, estimate_pairwise = FALSE, n.permut = 1000 )"},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — interaction.table","text":"al alteration matrix als alteration matrix stats object obs observed overlap wobs weighted observed overlap r.obs random observed overlap r.wobs random weighted observed overlap null null model maxFDR maxFDR cutoff n.cores number cores estimate_pairwise Compute pairwise n.permut number permutation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/interaction.table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — interaction.table","text":"table results","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_maf.html","id":null,"dir":"Reference","previous_headings":"","what":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","title":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","text":"MAF file LUAD TCGA","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_maf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","text":"","code":"data(luad_maf)"},{"path":"https://csogroup.github.io/SelectSim/reference/luad_maf.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Lung adenocarcinoma MAF from TCGA cohort — luad_maf","text":"dataframe","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","title":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","text":"Result LUAD generated selectX selectX run done min.freq=10.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","text":"","code":"data(luad_result)"},{"path":"https://csogroup.github.io/SelectSim/reference/luad_result.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Lung adenocarcinoma from TCGA cohort as selectX run results — luad_result","text":"dataframe","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_run_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","title":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","text":"dataset containing genome alteration matrix tumor mutation burden along sample,alteration annotation list object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/luad_run_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","text":"","code":"data(luad_run_data)"},{"path":"https://csogroup.github.io/SelectSim/reference/luad_run_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Lung adenocarcinoma from TCGA cohort as selectX run object — luad_run_data","text":"list object GAMs TMBs along sample & alteration annotations.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate gam from the maf file — maf2gam","title":"Generate gam from the maf file — maf2gam","text":"maf2gam() takes maf file converts gam","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate gam from the maf file — maf2gam","text":"","code":"maf2gam( maf, sample.col = \"Tumor_Sample_Barcode\", gene.col = \"Hugo_Symbol\", value.var = \"HGVSp_Short\", samples = NULL, genes = NULL, fun.aggregate = length, binarize = TRUE, fill = NA, ... )"},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate gam from the maf file — maf2gam","text":"maf maf dataframe sample.col list containing elements filter gene.col column maf file filter value.var column maf file filter samples column maf file filter genes column maf file filter fun.aggregate column maf file filter binarize boolena include exclude dataframe values list provided fill grep argument specify grep use argumnet string ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/maf2gam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate gam from the maf file — maf2gam","text":"filtered_maf GAM matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/mutation_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Mutation list object — mutation_type","title":"Mutation list object — mutation_type","text":"Mutation list object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/mutation_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mutation list object — mutation_type","text":"","code":"mutation_type"},{"path":"https://csogroup.github.io/SelectSim/reference/mutation_type.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Mutation list object — mutation_type","text":"object class list length 3.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an AL object — new.AL.general","title":"Create an AL object — new.AL.general","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an AL object — new.AL.general","text":"","code":"new.AL.general( am, feat.covariates = NULL, sample.covariates = NULL, min.freq, verbose = FALSE )"},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an AL object — new.AL.general","text":"binary alteration matrix row features column samples. feat.covariates gene/feature covariate. sample.covariates sample covariate. min.freq minimum frequency genes mutated. verbose print time steps.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AL.general.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an AL object — new.AL.general","text":"Alteration Landscape (AL) object gam.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration landscape object — new.ALS","title":"Create an alteration landscape object — new.ALS","text":"Create alteration landscape object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration landscape object — new.ALS","text":"","code":"new.ALS(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration landscape object — new.ALS","text":"al alteration landscape","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.ALS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration landscape object — new.ALS","text":"AlS object.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an alteration matrix stats object — new.AMS","title":"Create an alteration matrix stats object — new.AMS","text":"Create alteration matrix stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an alteration matrix stats object — new.AMS","text":"","code":"new.AMS(am)"},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an alteration matrix stats object — new.AMS","text":"alteration matrix stats object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/new.AMS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an alteration matrix stats object — new.AMS","text":"AMS object.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the null_simulation matrix — null_model_parallel","title":"Generating the null_simulation matrix — null_model_parallel","text":"Generating null_simulation matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the null_simulation matrix — null_model_parallel","text":"","code":"null_model_parallel(al, temp_mat, W, n.cores = 1, n.permut)"},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the null_simulation matrix — null_model_parallel","text":"al Alteration landscape object temp_mat template matrixes W weight matrix n.cores Number cores n.permut Number simulation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the null_simulation matrix — null_model_parallel","text":"Template matrix list object Ordering genes impacts results residual subraction correct.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the null_simulation matrix — null_model_parallel_debug","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"Generating null_simulation matrix","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"","code":"null_model_parallel_debug(al, temp_mat, W, n.cores = 1, n.permut)"},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"al Alteration landscape object temp_mat template matrixes W weight matrix n.cores Number cores n.permut Number simulation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/null_model_parallel_debug.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the null_simulation matrix — null_model_parallel_debug","text":"Template matrix list object Ordering genes impacts results residual subraction correct.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an AL object — obs_exp_scatter","title":"Create an AL object — obs_exp_scatter","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an AL object — obs_exp_scatter","text":"","code":"obs_exp_scatter(result, title)"},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an AL object — obs_exp_scatter","text":"result result table selectX obj$result title title plot","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/obs_exp_scatter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an AL object — obs_exp_scatter","text":"ggplot2 object observed vs random overlap plot.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"OncoKB v3.9 cancer genes — oncokb_genes","title":"OncoKB v3.9 cancer genes — oncokb_genes","text":"cancer genes list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OncoKB v3.9 cancer genes — oncokb_genes","text":"","code":"data(oncokb_genes)"},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_genes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"OncoKB v3.9 cancer genes — oncokb_genes","text":"list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_truncating_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","title":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","text":"cancer genes list consider truncating mutations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_truncating_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","text":"","code":"data(oncokb_truncating_genes)"},{"path":"https://csogroup.github.io/SelectSim/reference/oncokb_truncating_genes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"OncoKB v3.9 cancer genes consider for truncating mutations — oncokb_truncating_genes","text":"list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract the backgroun distribution — overlap_pair_extract","title":"Extract the backgroun distribution — overlap_pair_extract","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract the backgroun distribution — overlap_pair_extract","text":"","code":"overlap_pair_extract(gene1, gene2, obj)"},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract the backgroun distribution — overlap_pair_extract","text":"gene1 gene1 gene2 gene2 obj selectX obj","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/overlap_pair_extract.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract the backgroun distribution — overlap_pair_extract","text":"backgorund distribution vector.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"","code":"r.am.pairwise.alteration.overlap(null, n.permut, n.cores = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"null null model n.permut number permutation steps n.cores number cores","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.am.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — r.am.pairwise.alteration.overlap","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — r.effectSize","title":"Compute weight overlap stats — r.effectSize","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — r.effectSize","text":"","code":"r.effectSize(null_overlap, mean_mat, n.permut = 1000, n.cores = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — r.effectSize","text":"null_overlap null model overlap mean_mat mean effect size vector n.permut number permutation steps n.cores number cores","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/r.effectSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — r.effectSize","text":"overlap weight overlap pairs","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":null,"dir":"Reference","previous_headings":"","what":"Removing the Outliers — retrieveOutliers","title":"Removing the Outliers — retrieveOutliers","text":"Removing Outliers","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removing the Outliers — retrieveOutliers","text":"","code":"retrieveOutliers(obj, nSim = 1000)"},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removing the Outliers — retrieveOutliers","text":"obj selectX object nSim Number simulation","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/retrieveOutliers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Removing the Outliers — retrieveOutliers","text":"outliers","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a pairs background plot — ridge_plot_ed","title":"Generate a pairs background plot — ridge_plot_ed","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a pairs background plot — ridge_plot_ed","text":"","code":"ridge_plot_ed(result_df, obj)"},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a pairs background plot — ridge_plot_ed","text":"result_df result table selectX obj$result obj selectX obj","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a pairs background plot — ridge_plot_ed","text":"ggplot2 object observed vs random overlap plot.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"Create Alteration Landscape (AL) object contains gams mutation burden samples associated gams.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"","code":"ridge_plot_ed_compare(result_df, obj1, obj2, name1, name2)"},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"result_df common result table selectX obj$result dataset1_w_overlap dataset2_w_overlap columns obj1 selectX obj dataset1 obj2 selectX obj dataset2 name1 dataset1 name name2 dataset2 name","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/ridge_plot_ed_compare.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a pairs background plot for two dataset comaprision — ridge_plot_ed_compare","text":"ggplot2 object observed vs random overlap plot.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":null,"dir":"Reference","previous_headings":"","what":"SelectX main function to create alteration object with background model — selectX","title":"SelectX main function to create alteration object with background model — selectX","text":"selectX() takes list object consist genome alteration matrix tumor mutation burden.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SelectX main function to create alteration object with background model — selectX","text":"","code":"selectX( M, sample.class, alteration.class, n.cores = 1, min.freq = 10, n.permut = 1000, lambda = 0.3, tao = 1, save.object = FALSE, folder = \"./\", verbose = TRUE, estimate_pairwise = FALSE, maxFDR = 0.25, seed = 42 )"},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SelectX main function to create alteration object with background model — selectX","text":"M list data object consist gams tmbs. sample.class sample covariates named list. alteration.class alteration covariates named list. n.cores cores. min.freq number samples features atleast mutated . n.permut number simulations. lambda lambda parameter. tao tao parameter. save.object store SelectX object. folder folder path store results. verbose print time steps. estimate_pairwise Compute pairwise p-value maxFDR FDR value seed random seed","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"SelectX main function to create alteration object with background model — selectX","text":"result SelectX object background model info along result table","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":null,"dir":"Reference","previous_headings":"","what":"SelectX main function to create alteration object with background model — selectX_debug","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"selectX() takes list object consist genome alteration matrix tumor mutation burden.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"","code":"selectX_debug( M, sample.class, alteration.class, n.cores = 1, min.freq = 10, n.permut = 1000, lambda = 0.3, tao = 1, save.object = FALSE, folder = \"./\", verbose = TRUE, estimate_pairwise = FALSE, maxFDR = 0.25, seed = 42 )"},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"M list data object consist gams tmbs. sample.class sample covariates named list. alteration.class alteration covariates named list. n.cores cores. min.freq number samples features atleast mutated . n.permut number simulations. lambda lambda parameter. tao tao parameter. save.object store SelectX object. folder folder path store results. verbose print time steps. estimate_pairwise Compute pairwise p-value maxFDR FDR value seed random seed","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/selectX_debug.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"SelectX main function to create alteration object with background model — selectX_debug","text":"result SelectX object background model info along result table","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary functions for MAF file — stat_maf_column","title":"Summary functions for MAF file — stat_maf_column","text":"stat_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary functions for MAF file — stat_maf_column","text":"","code":"stat_maf_column(maf, column, ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary functions for MAF file — stat_maf_column","text":"maf maf dataframe column schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_column.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary functions for MAF file — stat_maf_column","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary functions for MAF file — stat_maf_gene","title":"Summary functions for MAF file — stat_maf_gene","text":"stat_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary functions for MAF file — stat_maf_gene","text":"","code":"stat_maf_gene(maf, column = \"Hugo_Symbol\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary functions for MAF file — stat_maf_gene","text":"maf maf dataframe column schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_gene.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary functions for MAF file — stat_maf_gene","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary functions for MAF file — stat_maf_sample","title":"Summary functions for MAF file — stat_maf_sample","text":"stat_maf_column() takes maf file filters MAF dataframe retaining rows column value included values list","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary functions for MAF file — stat_maf_sample","text":"","code":"stat_maf_sample(maf, column = \"Tumor_Sample_Barcode\", ...)"},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary functions for MAF file — stat_maf_sample","text":"maf maf dataframe column schema datafrane check Select::TCGA_maf_schema example ... options","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/stat_maf_sample.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary functions for MAF file — stat_maf_sample","text":"filtered_maf filtered maf file","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":null,"dir":"Reference","previous_headings":"","what":"Generating the template matrix — templeate.obj.gen","title":"Generating the template matrix — templeate.obj.gen","text":"Computing expected mutation background matrix using simulation done.","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generating the template matrix — templeate.obj.gen","text":"","code":"templeate.obj.gen(al)"},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generating the template matrix — templeate.obj.gen","text":"al Alteration landscape object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/templeate.obj.gen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generating the template matrix — templeate.obj.gen","text":"Template matrix list object","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/variant_catalogue.html","id":null,"dir":"Reference","previous_headings":"","what":"OncoKB v3.9 cancer genes — variant_catalogue","title":"OncoKB v3.9 cancer genes — variant_catalogue","text":"dataframe cancer genes missense mutation annotations","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/variant_catalogue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OncoKB v3.9 cancer genes — variant_catalogue","text":"","code":"data(variant_catalogue)"},{"path":"https://csogroup.github.io/SelectSim/reference/variant_catalogue.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"OncoKB v3.9 cancer genes — variant_catalogue","text":"dataframe","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"Compute weight overlap stats","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"","code":"w.r.am.pairwise.alteration.overlap(null, W, n.permut, n.cores = 1)"},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"null null model W weight matrix n.permut number permutation steps n.cores number cores","code":""},{"path":"https://csogroup.github.io/SelectSim/reference/w.r.am.pairwise.alteration.overlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute weight overlap stats — w.r.am.pairwise.alteration.overlap","text":"overlap weight overlap pairs","code":""},{"path":[]}]