clusterProfiler (version 2.4.1)

gseKEGG: gseKEGG

Description

Gene Set Enrichment Analysis of KEGG

Usage

gseKEGG(geneList, organism = "human", exponent = 1, nPerm = 1000, minGSSize = 10, pvalueCutoff = 0.05, pAdjustMethod = "BH", use_internal_data = FALSE, verbose = TRUE)

Arguments

geneList

order ranked geneList

organism

One of "anopheles", "arabidopsis", "bovine", "canine", "chicken", "chimp", "ecolik12","ecsakai", "fly", "human", "malaria", "mouse", "pig", "rat","rhesus", "worm", "xenopus", "yeast" and "zebrafish".

exponent

weight of each step

nPerm

permutation numbers

minGSSize

minimal size of each geneSet for analyzing

pvalueCutoff

pvalue Cutoff

pAdjustMethod

pvalue adjustment method

use_internal_data

whether use KEGG.db or not

verbose

print message or not

Value

gseaResult object