arseq.gsea.runall: Bulk Gene Set Enrichment Analysis (GSEA)

In ajitjohnson/arseq: Automated RNA Sequencing Analysis Pipeline

Description

Performing GSEA enrichment analysis on a ranked list of genes for all msigDB.

Usage

arseq.gsea.runall(
  ranked.list,
  save = FALSE,
  custom.gsea = NULL,
  save.dir = getwd()
)

Arguments

ranked.list	Ranked list of genes for GSEA analysis. Use 'arseq.gsea.preprocess' to generate ranked list of genes from DESeq2 differential gene expression analysis.
save	Logical. Argument to indicate if to save the results in disk (pdf and csv files). Default=FALSE
custom.gsea	User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list.
save.dir	Directory to save the results when 'save=TRUE'. Default= Working Directory.

Value

List containing all the GSEA dataframe and ggplot objects.

Examples

## Not run: 
ranked.list <- arseq.gsea.preprocess (deg=example_deg)
gsea.output <- arseq.gsea.runall (ranked.list)

## End(Not run)

ajitjohnson/arseq documentation built on Oct. 28, 2021, 3:53 a.m.