enrichGO2 {signatureSearch} | R Documentation

## GO Term Enrichment with Hypergeometric Test

### Description

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

### Usage

    enrichGO2(
      gene,
      OrgDb,
      keytype = "SYMBOL",
      ont = "MF",
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      universe,
      qvalueCutoff = 0.2,
      minGSSize = 5,
      maxGSSize = 500,
      pool = FALSE
    )

### Arguments

`gene` | a vector of gene SYMBOL ids (here the test set)
`OrgDb` | OrgDb
`keytype` | Gene ID type of test set
`ont` | One of "MF", "BP", "CC" or "ALL"
`pvalueCutoff` | pvalue cutoff
`pAdjustMethod` | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe` | background genes
`qvalueCutoff` | qvalue cutoff
`minGSSize` | minimum size of each gene set in annotation system
`maxGSSize` | maximum size of each gene set in annotation system
`pool` | If ont='ALL', whether 3 GO ontologies should be combined

### Value

A `feaResult` instance.

### See Also

`feaResult-class`

### Examples

    # The method supports duplicated elements in 'gene',
    # which should be gene SYMBOL ids for GO term enrichment.
    gene <- c(rep("HDAC1",4), rep("HDAC3",2), "SOX8", "KLK14")
    # data(targetList)
    # ego <- enrichGO2(gene = gene, OrgDb="org.Hs.eg.db", ont="MF",
    #                  universe=names(targetList))

[Package signatureSearch version 1.1.5 Index]