update Get_CorrectBg_p

.Rhistory

@@ -1,27 +1,3 @@
-scale_colour_gradient2(low="#3A71AA",mid="white",high="#B22028",midpoint=0)+
-theme_bw()+
-theme (axis.text.x = element_text (angle = 45, hjust = 1))+theme(legend.position = "top")
-pdf("D:\\OneDrive\\类器官空间\\DEanalysis\\celltypemarker_chenming8.4check_dotplot.pdf",width = 14,height = 4)
-DotPlot(scdata,features=unique(GENES),group.by="New_celltype",assay="SCT")+
-scale_colour_gradient2(low="#3A71AA",mid="white",high="#B22028",midpoint=0)+
-theme_bw()+
-theme (axis.text.x = element_text (angle = 45, hjust = 1))+theme(legend.position = "top")
-dev.off()
-library(Seurat)
-library(dplyr)
-library(ggplot2)
-library(patchwork)
-library(ggpubr)
-scdata<-readRDS("D:\\OneDrive\\类器官空间\\DEanalysis\\H9_D60_2_stdata.rds")
-scdata<-subset(scdata,subset = seurat_clusters!=6 & seurat_clusters!=7)
-scdata$seurat_clusters<-as.character(scdata$seurat_clusters)
-scdata$seurat_clusters[scdata$seurat_clusters==0]<-6
-scdata$New_celltype<-scdata$seurat_clusters
-table(scdata$New_celltype)
-scdata$New_celltype[scdata$New_celltype=="6"]<-"RPC/PC"
-scdata$New_celltype[scdata$New_celltype=="1"]<-"RGC/RPC"
-scdata$New_celltype[scdata$New_celltype=="2"]<-"RPC/PC_precursors/MC"
-scdata$New_celltype[scdata$New_celltype=="3"]<-"RPE/RPE_progenitors"
 scdata$New_celltype[scdata$New_celltype=="4"]<-"hRSLCs"
 scdata$New_celltype[scdata$New_celltype=="5"]<-"RPC/PC/AC_HC/BC/MC"
 saveRDS(scdata,"D:\\OneDrive\\类器官空间\\DEanalysis\\H9_D60_2_final_stdata.rds")
@@ -510,3 +486,27 @@ celltype=T# Whether to run the celltype process.
 ##------ Wed Aug 23 16:06:04 2023 ------##
 ##------ Wed Aug 23 16:06:05 2023 ------##
 ##------ Wed Aug 23 16:06:07 2023 ------##
+devtools::load_all(".")
+Pagwas_data<-scPagwas_main(Pagwas = NULL,
+gwas_data =system.file("extdata", "GWAS_summ_example.txt", package = "scPagwas"), # The GWAS Summary statistics files
+Single_data =system.file("extdata", "scRNAexample.rds", package = "scPagwas"),# scRNA-seq data in seruat format with "RNA" assays and normalized.
+output.prefix="test", # the prefix name for output files
+output.dirs="scPagwastest_output",# the directory file's name for output
+block_annotation = block_annotation,# gene position in chromosome is provided by package.
+assay="RNA", # the assays for scRNA-seq data to use.
+Pathway_list=Genes_by_pathway_kegg,# pathway list is provided by package, including gene symbols.
+n.cores=1,
+iters_singlecell = 10,
+chrom_ld = chrom_ld,# The LD data is provided by package.
+singlecell=T, # Whether to run the singlecell process.
+celltype=T# Whether to run the celltype process.
+)
+##------ Mon Aug 28 10:13:27 2023 ------##
+##------ Mon Aug 28 10:13:32 2023 ------##
+##------ Mon Aug 28 10:14:06 2023 ------##
+##------ Mon Aug 28 10:14:06 2023 ------##
+##------ Mon Aug 28 10:14:06 2023 ------##
+##------ Mon Aug 28 10:14:08 2023 ------##
+##------ Mon Aug 28 10:14:17 2023 ------##
+##------ Mon Aug 28 10:14:18 2023 ------##
+##------ Mon Aug 28 10:14:20 2023 ------##

R/Get_CorrectBg_p.R

@@ -7,8 +7,8 @@
 #' @param scPagwas_topgenes gene list
 #' @return correct_pdf
 #' @export
-Get_CorrectBg_p<-function(Single_data,scPagwas.TRS.Score, iters_singlecell,n_topgenes,scPagwas_topgenes){
-    gene_matrix <- GetAssayData(Single_data, slot = "data", assay = 'RNA')
+Get_CorrectBg_p<-function(Single_data,scPagwas.TRS.Score, iters_singlecell,n_topgenes,scPagwas_topgenes,assay){
+    gene_matrix <- GetAssayData(Single_data, slot = "data", assay = assay)
     mat_ctrl_raw_score <- matrix(0, nrow =ncol(gene_matrix), ncol = iters_singlecell)
     dic_ctrl_list <- list()
     pb <- txtProgressBar(style = 3)
@@ -17,7 +17,7 @@ Get_CorrectBg_p<-function(Single_data,scPagwas.TRS.Score, iters_singlecell,n_top
         set.seed(i)
         dic_ctrl_list[[i]] <- sample(rownames(Single_data), n_topgenes)
         Single_data<-Seurat::AddModuleScore(Single_data,
-            assay = 'RNA',
+            assay = assay,
             list(dic_ctrl_list[[i]]),
             name = c("contr_genes")
             )

R/scPagwas_main.R

@@ -588,7 +588,8 @@ scPagwas_main <- function(Pagwas = NULL,
                                  scPagwas.TRS.Score=Single_data$scPagwas.TRS.Score1,
                                  iters_singlecell=iters_singlecell,
                                  n_topgenes=n_topgenes,
-                                 scPagwas_topgenes=scPagwas_topgenes
+                                 scPagwas_topgenes=scPagwas_topgenes,
+                                 assay=assay
     )
     Pagwas$Random_Correct_BG_pdf <- correct_pdf
     message("* Get Merged pvalue for each celltype!")