enrichDO {DOSE} | R Documentation

## DO Enrichment Analysis

### Description

Given a vector of genes, this function will return the enrichment DO categories with FDR control.

### Usage

    enrichDO(
      gene,
      ont = "DO",
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      universe,
      minGSSize = 10,
      maxGSSize = 500,
      qvalueCutoff = 0.2,
      readable = FALSE
    )

### Arguments

`gene` | a vector of entrez gene id
`ont` | one of DO or DOLite.
`pvalueCutoff` | pvalue cutoff
`pAdjustMethod` | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe` | background genes
`minGSSize` | minimal size of genes annotated by NCG category for testing
`maxGSSize` | maximal size of each geneSet for analyzing
`qvalueCutoff` | qvalue cutoff
`readable` | whether mapping gene ID to gene Name

### Value

A `enrichResult` instance.

### Author(s)

Guangchuang Yu http://guangchuangyu.github.io

### See Also

`enrichResult-class`

### Examples

    data(geneList)
    	gene = names(geneList)[geneList > 1]
    	yy = enrichDO(gene, pvalueCutoff=0.05)
    	summary(yy)

[Package DOSE version 3.16.0 Index]