getgo: Fetch GO categories

In nadiadavidson/goseq: Gene Ontology analyser for RNA-seq and other length biased data

Description

Obtains all gene ontology (GO) categories associated with a set of genes using the relevant organism package.

Usage

getgo(genes, genome, id,fetch.cats=c("GO:CC","GO:BP","GO:MF"))

Arguments

genes	A vector or list of genes to get the associated GO categories.
genome	A string identifying the genome that genes refer to. For a list of supported organisms run supportedGenomes.
id	A string identifying the gene identifier used by genes. For a list of supported gene IDs run supportedGeneIDs.
fetch.cats	A vector specifying which categories to fetch the mapping between category names and genes for. See details for vaild options.

Details

This function attempts to make use of the organism packages (org.<Genome>.<GeneID>.db) to obtain the mapping between gene ID and GO categories. As with getlength it is preferable that the same gene identifier system is used for both summarization and retrieving GO categories.

Valid options for the fetch.cats arguement are any combination of "GO:CC", "GO:BP", "GO:MF" & "KEGG". The three GO terms refer to the Cellular Component, Biological Process and Molecular Function respectively. "KEGG" refers to KEGG pathways.

Note that getgo is a convenience function, designed to make extracting mappings between GO categories and Gene ID easy. For less common organisms and/or gene ID getgo may fail to return a mapping even when a legitimate mapping exists in the revelant organism package. If getgo fails, you should always try to build the mapping yourself from the organism package (if one exists) before deciding that the information is unavailable. Further information and examples of this can be found in the package Vignette.

Value

A list where each entry is named by a gene and contains a vector of all the associated GO categories. This can be used directly with the gene2cat option in goseq.

Author(s)

Matthew D. Young [e-mail]

See Also

supportedGenomes, supportedGeneIDs, goseq

Examples

genes <- c("ENSG00000124208", "ENSG00000182463", "ENSG00000124201", "ENSG00000124205", "ENSG00000124207")
getgo(genes,'hg19','ensGene')

nadiadavidson/goseq documentation built on Oct. 28, 2019, 10:27 a.m.