gseKEGG2 {signatureSearch} | R Documentation

## Modified GSEA with KEGG

### Description

This modified Gene Set Enrichment Analysis (GSEA) of KEGG pathways supports gene test sets with large numbers of zeros.

### Usage

    gseKEGG2(
      geneList,
      organism = "hsa",
      keyType = "kegg",
      exponent = 1,
      nproc = 1,
      nPerm = 1000,
      minGSSize = 10,
      maxGSSize = 500,
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      verbose = TRUE
    )

### Arguments

`geneList` | named numeric vector with gene 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'
`exponent` | weight of each step
`nproc` | if not equal to zero, sets `BPPARAM` to use `nproc` workers (default = 1)
`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
`verbose` | print message or not

### Value

feaResult object

### Examples

    # Gene Entrez id should be used for KEGG enrichment
    data(geneList, package="DOSE")
    #geneList[100:length(geneList)]=0
    #gsekk <- gseKEGG2(geneList=geneList, pvalueCutoff = 1)
    #head(gsekk)

[Package signatureSearch version 1.0.4 Index]