FragPipeAnalystR

R package for FragPipe downstream analysis

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