GSEA_internal: GSEA_internal

In GuangchuangYu/DOSE: Disease Ontology Semantic and Enrichment analysis

GSEA_internal

Description

generic function for gene set enrichment analysis

Usage

GSEA_internal(
  geneList,
  exponent,
  minGSSize,
  maxGSSize,
  eps,
  pvalueCutoff,
  pAdjustMethod,
  verbose,
  seed = FALSE,
  USER_DATA,
  by = "fgsea",
  ...
)

Arguments

geneList	order ranked geneList
exponent	weight of each step
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of each geneSet for analyzing
eps	This parameter sets the boundary for calculating the p value.
pvalueCutoff	p value Cutoff
pAdjustMethod	p value adjustment method
verbose	print message or not
seed	set seed inside the function to make result reproducible. FALSE by default.
USER_DATA	annotation data
by	one of 'fgsea' or 'DOSE'
...	other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

GuangchuangYu/DOSE documentation built on Oct. 31, 2024, 9:15 a.m.