genGSEA: Gene Set Enrichment Analysis

In genekitr: Gene Analysis Toolkit

Gene Set Enrichment Analysis

Description

Gene Set Enrichment Analysis

Usage

genGSEA(
  genelist,
  geneset,
  padj_method = "BH",
  p_cutoff = 0.05,
  q_cutoff = 0.05,
  min_gset_size = 10,
  max_gset_size = 500,
  set_seed = FALSE
)

Arguments

genelist	Pre-ranked genelist with decreasing order, gene can be entrez, ensembl or symbol.
geneset	Gene set is a two-column data.frame with term id and gene id. Please use package 'geneset' to select available gene set or make new one.
padj_method	One of "BH", "BY", "bonferroni","fdr","hochberg", "holm", "hommel", "none"
p_cutoff	Numeric of cutoff for both unadjusted and adjusted pvalue, default is 0.05.
q_cutoff	Numeric of cutoff for qvalue, default is 0.05.
min_gset_size	Numeric of minimal size of each geneset for analyzing, default is 10.
max_gset_size	Numeric of maximal size of each geneset for analyzing, default is 500.
set_seed	GSEA permutations are performed using random reordering, which causes slightly difference results after every time running. If user want to get same result every time for same input, please set 'set_seed = TRUE' or 'set.seed()' prior to running.

Value

A 'data.frame'.

Examples

if(requireNamespace("geneset",quietly = TRUE)){
# only gene ids
data(geneList, package = "genekitr")
gs <- geneset::getGO(org = "human",ont = "mf",data_dir = tempdir())
gse <- genGSEA(genelist = geneList, geneset = gs)
  }

genekitr documentation built on Sept. 11, 2024, 9:10 p.m.