clusterProfiler (version 3.0.4)

gseKEGG: gseKEGG

Description

Gene Set Enrichment Analysis of KEGG

Usage

gseKEGG(geneList, organism = "hsa", keyType = "kegg", exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE, use_internal_data = FALSE, seed = FALSE)

Arguments

geneList

order ranked geneList

organism

supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'

keyType

one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'

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

use_internal_data

logical, use KEGG.db or latest online KEGG data

seed

logical

Value

gseaResult object