mabsKEGG: MeanAbs Enrichment Analysis for KEGG

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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.