minimalistGODB (version 1.0)

parseGOBASIC: parseGOBASIC

Description

parse go-basic.obo

Usage

parseGOBASIC(gobasic, verbose = FALSE)

Value

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

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/

Examples

if (FALSE) {
# 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"
}

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