GSEA: GSEA

In clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

Description

a universal gene set enrichment analysis tools

Usage

GSEA(
  geneList,
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  TERM2GENE,
  TERM2NAME = NA,
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  ...
)

Arguments

geneList	order ranked geneList
exponent	weight of each step
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of genes annotated for testing
eps	This parameter sets the boundary for calculating the p value.
pvalueCutoff	adjusted pvalue cutoff
pAdjustMethod	p value adjustment method
TERM2GENE	user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
TERM2NAME	user input of TERM TO NAME mapping, a data.frame of 2 column with term and name
verbose	logical
seed	logical
by	one of 'fgsea' or 'DOSE'
...	other parameter

Value

gseaResult object

Author(s)

Guangchuang Yu

clusterProfiler documentation built on Feb. 11, 2021, 2:02 a.m.