meshHyperGTest {meshr} | R Documentation

## Hypergeometric Tests for MeSH term association

### Description

Given a `MeSHHyperGParams` object containing a set of selected and background gene IDs, and gene-MeSH annotation data of interest, `meshHyperGTest` performs Hypergeomtric test for over-representation of each MeSH term accouting for the multiple testing correction.

### Arguments

`p` | A `MeSHHyperGParams` object

### Details

For details on creating `MeSHHyperGParams` object, please read the documentation in the MeSHHyperGParams-class.

### Value

A `MeSHHyperGResult` object.

### Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>

### See Also

`meshr-package`, `MeSHHyperGParams-class`, `MeSHHyperGResult-class`

### Examples

    data(geneid.cummeRbund)
    data(sig.geneid.cummeRbund)

    meshParams <- new("MeSHHyperGParams", geneIds=sig.geneid.cummeRbund[,2], universeGeneIds=geneid.cummeRbund[,2], annotation="MeSH.Hsa.eg.db", category="Z", database="gene2pubmed", pvalueCutoff=0.05, pAdjust="none")

    meshR <- meshHyperGTest(meshParams)

[Package meshr version 1.15.0 Index]