enrichMeSH {meshes} | R Documentation

## enrichMeSH

### Description

MeSH term enrichment analysis

### Usage

    enrichMeSH(
      gene,
      MeSHDb,
      database = "gendoo",
      category = "C",
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      universe,
      qvalueCutoff = 0.2,
      minGSSize = 10,
      maxGSSize = 500
    )

### Arguments

`gene` | a vector of entrez gene id
`MeSHDb` | MeSHDb
`database` | one of 'gendoo', 'gene2pubmed' or 'RBBH'
`category` | one of "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L","M", "N", "V", "Z"
`pvalueCutoff` | Cutoff value of pvalue.
`pAdjustMethod` | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe` | background genes
`qvalueCutoff` | qvalue cutoff
`minGSSize` | minimal size of genes annotated by Ontology term for testing.
`maxGSSize` | maximal size of genes annotated for testing

### Value

An `enrichResult` instance.

### Author(s)

Guangchuang Yu

### See Also

`class?enrichResult`

### Examples

    ## Not run:
    data(geneList, package="DOSE")
    de <- names(geneList)[1:100]
    x <- enrichMeSH(de, MeSHDb = "MeSH.Hsa.eg.db", database='gendoo', category = 'C')

    ## End(Not run)

[Package meshes version 1.18.1 Index]