sigGOTable: Obtain significant GO terms for a list of genes

In Ringo: R Investigation of ChIP-chip Oligoarrays

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)

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.