go2genes: Takes a list of GO ids and queries all the genes related to...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Takes a list of GO ids and queries all the genes related to it (including the ones for child nodes)

Description

Takes a list of GO ids and queries all the genes related to it (including the ones for child nodes)

Usage

go2genes(goID, annotGO, pathGeneMap, queryList, GOList, ontology,
  exportAnnotGO = TRUE, exportGOList = TRUE, verbose = FALSE, ...)

Arguments

goID	list of GO ids to retrieve the genes for
annotGO	optional; data.frame with information of the go ids and the related genes
pathGeneMap	path to the file for the annotGO
queryList	argument for createAnnot if no annotGO or pathGeneMap are not provided
GOList	GO ids related to the list of the provided GO ids (such as their child nodes)
ontology	one from 'BP','CC' or 'MF'
exportAnnotGO	logical; whether annotGO should be exported to the environement sharedenv for future use
exportGOList	logical; whether GOList should be exported to the environement sharedenv for future use
verbose	logical; allows to better track how annotGO and GOList are created/used
...	other argument to pass to createGoAnnot

Value

Gene list associated to the GO ids

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.