mabsKEGG {signatureSearch} | R 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)

[Package signatureSearch version 1.6.3 Index]