mabsKEGG: MeanAbs Enrichment Analysis for KEGG

View source: R/mabsAnalyser.R

mabsKEGGR Documentation

MeanAbs Enrichment Analysis for KEGG

Description

MeanAbs enrichment analysis with KEGG pathways.

Usage

mabsKEGG(
  geneList,
  organism = "hsa",
  keyType = "kegg",
  nPerm = 1000,
  minGSSize = 5,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  readable = FALSE
)

Arguments

geneList

named numeric vector with gene/target ids in the name slot decreasingly ranked by scores in the data slot.

organism

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

keyType

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

nPerm

permutation numbers

minGSSize

integer, minimum size of each gene set in annotation system

maxGSSize

integer, maximum size of each gene set in annotation system

pvalueCutoff

pvalue cutoff

pAdjustMethod

pvalue adjustment method

readable

TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

Value

feaResult object

Examples

# Gene Entrez id should be used for KEGG enrichment
data(geneList, package="DOSE")
#geneList[100:length(geneList)]=0
#mk <- mabsKEGG(geneList=geneList, pvalueCutoff = 1)
#head(mk)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.