gseKEGG: gseKEGG

In GuangchuangYu/clusterProfiler: A universal enrichment tool for interpreting omics data

gseKEGG

Description

Gene Set Enrichment Analysis of KEGG

Usage

gseKEGG(
  geneList,
  organism = "hsa",
  keyType = "kegg",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  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 'https://www.genome.jp/kegg/catalog/org_list.html'
keyType	one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
exponent	weight of each step
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of genes annotated for testing
eps	This parameter sets the boundary for calculating the p value.
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'
...	other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

GuangchuangYu/clusterProfiler documentation built on Nov. 30, 2024, 3:25 a.m.