GSEA: Gene Set Enrichment Analysis

In kevincjnixon/BinfTools: Useful functions for standard analyses

Gene Set Enrichment Analysis

Description

Perform a GSEA using fgsea and gage analyses

Usage

GSEA(
  rnk,
  gmt,
  pval = 1,
  ts = c(10, 600),
  nperm = 10000,
  parseBader = TRUE,
  plot.title = "Gene Set Enrichment Analysis",
  useGAGE = TRUE
)

Arguments

rnk	named vector of gene rankings (names are genes with matching nomenclature of geneset file)
gmt	named list of gene sets or character indicating gmt file path for gene sets to be used in GSEA analysis
pval	Adjusted p-value threshold to filter results. Set to 1 to return all results. Default=1
ts	numeric vector of length two indicating the minimum and maximum gene set sizes
nperm	integer indicating number of permutations to run. Default is 10000
parseBader	Boolean indicating if gene set names should be parsed for the output figure following Bader Lab nomenclature (i.e. '%' as delimiter)
plot.title	Title for the plot
useGAGE	Boolean indicating if GAGE results should be used to filter fgsea results. Default=TRUE

Value

A data frame of GSEA results and a figure showing normalized enrichment scores (NES) for top positive and negative enriched gene sets.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.