arseq.gsea: Gene Set Enrichment Analysis (GSEA)

In ajitjohnson/arseq: Automated RNA Sequencing Analysis Pipeline

Description

Performing GSEA enrichment analysis on a ranked list of genes.

Usage

arseq.gsea(
  ranked.list,
  custom.gsea = NULL,
  f.name = "GeneSet",
  fsub.name = "enrichment",
  category = NULL,
  subcategory = NULL,
  save = FALSE,
  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.
custom.gsea	User defined gene list to perform GSEA. File need to be supplied as a dataframe with each row as a gene list
f.name	Folder name to save the results when 'save=TRUE'
fsub.name	File name of the results when 'save=TRUE'
category	collection, such as H, C1, C2, C3, C4, C5, C6, C7
subcategory	sub-collection, such as CGP, MIR, BP, etc
save	Logical. Argument to indicate if to save the results in disk (pdf and csv files). Default=FALSE
save.dir	Directory to save the results when 'save=TRUE'. Default= Working Directory.

Value

List containing a dataframe and a ggplot object.

Examples

ranked.list <- arseq.gsea.preprocess (deg=example_deg)
gsea.output <- arseq.gsea (ranked.list, category = "H")

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