minimalistGODB (version 1.0)

buildGODatabase: buildGODatabase

Description

driver to build GO database

Usage

buildGODatabase(goa, gobasic, dir = NULL, verbose = FALSE)

Value

returns GO database with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")

Arguments

goa

character string path name to downloaded goa_human.gaf

gobasic

character string path name to downloaded go-basic.obo

dir

character string path name to directory to hold subdirectory GODB_RDATA

verbose

Boolean if TRUE print out some diagnostic info

Details

download goa_human.gaf from https://current.geneontology.org/products/pages/downloads.html download go-basic.obo from https://geneontology.org/docs/download-ontology/ parameter dir should be omitted or NULL except for the developer harvesting the updated .RData DBs

The output GOGOA was saved as an .RData file. This was too large for CRAN. It is available from https://github.com/barryzee/GO

Examples

if (FALSE) {
# replace my path names for goa and gobasic with your own!!
# these were obtained from the download sites listed in 'details' section
goa<-"~/goa_human.gaf"
gobasic<-"~/go-basic.obo"
GOGOA<-buildGODatabase(goa,gobasic,dir="~/",verbose=FALSE)
# > dim(GOGOA)
# [1] 720139      5
# > GOGOA[1:5,]
#      HGNC          GO           RELATION      NAME                    ONTOLOGY            
# [1,] "NUDT4B"      "GO:0003723" "enables"     "RNA binding"           "molecular_function"
# [2,] "NUDT4B"      "GO:0005515" "enables"     "protein binding"       "molecular_function"
# [3,] "NUDT4B"      "GO:0046872" "enables"     "metal ion binding"     "molecular_function"
# [4,] "NUDT4B"      "GO:0005829" "located_in"  "cytosol"               "cellular_component"
# [5,] "TRBV20OR9-2" "GO:0002376" "involved_in" "immune system process" "biological_process"
}

# here is a small example that you can run
f1<-system.file("extdata","goa_human.small.gaf",package="minimalistGODB")
f2<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
GODBsmall<-buildGODatabase(f1,f2,verbose=FALSE)