parseGOBASIC: parseGOBASIC

In minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB)

parseGOBASIC

Description

parse go-basic.obo

Usage

parseGOBASIC(gobasic, verbose = FALSE)

Arguments

gobasic	character string path name to downloaded go-basic.obo
verbose	Boolean if TRUE print out some diagnostic info

Details

download go-basic.obo from https://geneontology.org/docs/download-ontology/

Value

returns a list whose components are c("m", "bp", "mf", "cc")

Examples

## Not run: 
# replace my path name for gobasic with your own!!
# this was obtained from the download sites listed in 'details' section
GO<-parseGOBASIC("~/go-basic.obo",verbose=FALSE)
# GO$bp[1:5,]
#            GO           NAME                               ONTOLOGY            
# GO:0000001 "GO:0000001" "mitochondrion inheritance"        "biological_process"
# GO:0000002 "GO:0000002" "mitochondrial genome maintenance" "biological_process"
# GO:0000011 "GO:0000011" "vacuole inheritance"              "biological_process"
# GO:0000012 "GO:0000012" "single strand break repair"       "biological_process"
# GO:0000017 "GO:0000017" "alpha-glucoside transport"        "biological_process"

## End(Not run)

# here is a small example that you can run
f<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
GOsmall<-parseGOBASIC(f)

minimalistGODB documentation built on June 8, 2025, 11:41 a.m.