gseKEGG: gseKEGG

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

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, 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
use_internal_data	logical, use KEGG.db or latest online KEGG data
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.