gseGO: gseGO

In aiminy/ModifiedclusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

Description

Gene Set Enrichment Analysis of Gene Ontology

Usage

gseGO(geneList, ont = "BP", OrgDb, keytype = "ENTREZID", exponent = 1,
  nPerm = 1000, minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05,
  pAdjustMethod = "BH", verbose = TRUE, seed = FALSE, by = "fgsea")

Arguments

geneList	order ranked geneList
ont	one of "BP", "MF", "CC" or "GO"
OrgDb	OrgDb
keytype	keytype of gene
exponent	weight of each step
nPerm	permutation numbers
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of genes annotated for testing
pvalueCutoff	pvalue Cutoff
pAdjustMethod	pvalue adjustment method
verbose	print message or not
seed	logical
by	one of 'fgsea' or 'DOSE'

Value

gseaResult object

Author(s)

Yu Guangchuang

aiminy/ModifiedclusterProfiler documentation built on May 10, 2019, 7:37 a.m.