gseMKEGG: gseMKEGG

Description Usage Arguments Value Author(s)

View source: R/gseAnalyzer.R

Description

Gene Set Enrichment Analysis of KEGG Module

Usage

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

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

seed

logical

by

one of 'fgsea' or 'DOSE'

Value

gseaResult object

Author(s)

Yu Guangchuang


Bioconductor-mirror/clusterProfiler documentation built on July 28, 2017, 5:21 a.m.