sigGOTable {Ringo} | R Documentation

## Obtain significant GO terms for a list of genes

### Description

Function to obtain a table of significant GO terms given a list of genes, for example: genes related to ChIP-enriched regions.

### Usage

    sigGOTable(selGenes, universeGenes, annotType="list",
               ontology="BP", maxP=0.001, algorithm="elim",
               minGenes=10, gene2GO=list(), pkg="org.Mm.eg.db", ...)

### Arguments

`selGenes` | character; names of the genes in the list; must correspond to the names of the list `gene2GO` (if annotType is “list”) or to Entrezgene identifiers (if annotType is “org”).
`universeGenes` | character; names of the genes to focus the analysis on (if desired). Sometimes specifying a smaller list of genes as the background 'universe' may lead to more informative results from the Fisher test.
`annotType` | string; in which format is the GO annotation of the genes provided; either “list” if a named list (argument `gene2GO`) is provided OR “org” if one of the Entrezgene-based annotation packages, e.g. `org.Xx.eg.db`, shall be used
`ontology` | string; which ontology to use, one of “BP”, “MF”, or “CC”
`maxP` | numeric; which maximum p-value to allow for GO terms to be called significantly associated to the gene list; passed on topGO function `runTest` and used to subset the table of significant GO terms reported by topGO.
`algorithm` | string; one of ‘elim’, ‘classic’, ‘weight’, ‘topgo’, or ‘parentChild’; which method to use in the topGO analyis; see the topGO package for details.
`minGenes` | numeric; the required minimum number of genes (from `universeGenes`) that must be annotated for a GO term in order to consider it in the analysis; corresponds to the argument `nodeSize` in `topGO`
`gene2GO` | A list that contains for each gene the identifiers (GO:00001234...) of GO terms that are annotated for this gene; only used if `annotType=`“list”
`pkg` | Name of the Entrezgene-based annotation package to obtain the GO annotation from. Only used if `annotType=`“org”
`...` | additional arguments that are passed on to the constructor when building the `topGOdata` object.

### Details

This function is really just a convenience wrapper around functions in the `topGO` package.

It performs an exact Fisher-test and by default uses the ‘elim’ method of the `topGO` testing framework.

### Value

a `data.frame` containing the GO terms with p-values lower than the specified cut-off.

### Author(s)

Joern Toedling

### See Also

function `runTest` and the vignette in package `topGO`

### Examples

     ## Not run:
       library("topGO")
       library("hgu95av2.db")
       # get probe sets annotated for 'regulation of blood pressure'
       sel <- get("GO:0007616", hgu95av2GO2ALLPROBES)
       # create list that matches probe sets to GO
       ps2GO <- lapply(as.list(hgu95av2GO), names)

       sigGOTable(selGenes=sel, annotType="list", gene2GO=ps2GO)

    ## End(Not run)

[Package Ringo version 1.42.1 Index]