FragPipeAnalystR

R package for FragPipe downstream analysis

Check documentation including several tutorials to get started.

Installation

We recommend to use renv for managing your R environment dependencies

renv::install("bioc::ComplexHeatmap")
renv::install("bioc::limma")
renv::install("bioc::MSnbase")
renv::install("bioc::SummarizedExperiment")
renv::install("bioc::cmapR")
renv::install("bioc::ConsensusClusterPlus")
renv::install("Nesvilab/FragPipeAnalystR")

# optional
renv::install("nicolerg/ssGSEA2")

Example

library(FragPipeAnalystR)
data("ccrcc", package = "FragPipeAnalystR")

PCA

plot_pca(ccrcc)

Correlation heatmap

plot_correlation_heatmap(ccrcc)

Missing value heatmap

plot_missval_heatmap(ccrcc)

Feature numbers

plot_feature_numbers(ccrcc)

Box plot

plot_feature(ccrcc, c("CA9", "AHNAK2", "NDUFV2", "PIGR"))

Differential expression analysis

de_result <- test_limma(ccrcc, type = "all")
de_result_updated <- add_rejections(de_result)
plot_volcano(de_result_updated, "Tumor_vs_NAT")

Enrichment

or_result <- or_test(de_result_updated, database = "Hallmark", direction = "UP")
plot_or(or_result)

Developer guide

• Start project renv::init(): You may see message similar to this

* Using Bioconductor version '3.18'.
This project already has a lockfile. What would you like to do? 

1: Restore the project from the lockfile.
2: Discard the lockfile and re-initialize the project.
3: Activate the project without snapshotting or installing any packages.
4: Abort project initialization.

We recommend to choose 2 here to initialize the project since some dependencies depend on the R version and bioconductor version use

• You may use lintr::lint_package() and styler::style_pkg() to make sure coding styles consistent
• devtools::build() and devtools::test() to build and test the package, respectively
• devtools::document() when you add a function
• usethis::use_import_from("package name", "function name") to include dependencies
• devtools::build_rmd("./vignettes/*.Rmd") to build the tutorial Rmd file

Reference

Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, and Alexey I. Nesvizhskii Journal of Proteome Research (2024), DOI: 10.1021/acs.jproteome.4c00294