getgo | R Documentation |
Obtains all gene ontology (GO) categories associated with a set of genes using the relevant organism package.
getgo(genes, genome, id,fetch.cats=c("GO:CC","GO:BP","GO:MF"))
genes |
A vector or list of genes to get the associated GO categories. |
genome |
A string identifying the genome that |
id |
A string identifying the gene identifier used by |
fetch.cats |
A vector specifying which categories to fetch the mapping between category names and genes for. See details for vaild options. |
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.
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
.
Matthew D. Young myoung@wehi.edu.au
supportedGenomes
, supportedGeneIDs
, goseq
genes <- c("ENSG00000124208", "ENSG00000182463", "ENSG00000124201", "ENSG00000124205", "ENSG00000124207") getgo(genes,'hg19','ensGene')
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