enrichKEGG2 {signatureSearch} | R Documentation

## KEGG Pathway Enrichment with Hypergeometric Test

### Description

Given a vector of gene identifiers, this function returns KEGG pathway enrichment results based on a hypergeometric test with duplication support in the test set.

### Usage

    enrichKEGG2(
      gene,
      organism = "hsa",
      keyType = "kegg",
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      universe,
      minGSSize = 5,
      maxGSSize = 500,
      qvalueCutoff = 0.2,
      readable = FALSE
    )

### Arguments

`gene` | a vector of entrez gene ids (here the test set)
`organism` | supported organism are listed in http://www.genome.jp/kegg/catalog/org_list.html
`keyType` | one of "kegg", 'ncbi-geneid', 'ncbi-proteinid' or 'uniprot'
`pvalueCutoff` | pvalue cutoff
`pAdjustMethod` | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe` | background genes
`minGSSize` | minimal size of genes annotated by ontology term for testing.
`maxGSSize` | maximal size of genes annotated for testing
`qvalueCutoff` | qvalue cutoff
`readable` | TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

### Value

A `feaResult` instance.

### Examples

    # Method supports duplicated elements in "gene", which should be entrez ids
    gene <- c(rep("4312",4), rep("8318",2), "991", "10874")
    #data(geneList, package="DOSE")
    #kk <- enrichKEGG2(gene = gene, universe=names(geneList))
    #head(kk)

[Package signatureSearch version 1.4.6 Index]