geecc (version 1.0.0)

GO2list: Filter GO and KEGG database

Description

Filter GO and KEGG database and transforms database to list

Usage

GO2list(dbase, go.cat = NULL, rm = NULL, keep = NULL)
KEGG2list(dbase, rm = NULL, keep = NULL)

Arguments

dbase

A database (usually of class ‘ProbeGo3AnnDbBimap’ (as defined in package “AnnotationDbi”)) or named list containing GO or KEGG information

go.cat

GO category ("MF", "BP", "CC") that should be returned and filtered

rm

remove these terms

keep

keep only these terms

Value

A named list with each slot containing the ids for the term or pathway.

Details

The settings for “rm” and “keep” can be combined, allowing for efficient reduction of the number of GO terms and KEGG pathways, respectively.

Providing a named list instead of a database can be useful for non-model organisms, where only a draft Blast2GO-annotation is available. In this case, the names of the list are the GO terms (or KEGG pathways) and the content of each list item is a character vector with tag-ids.

Examples

library(hgu133plus2.db)
x <- GO2list(dbase=hgu133plus2GO2PROBE, go.cat="CC",
	rm=c("GO:0000139", "GO:0000790", "GO:0005730", "GO:0005739"))