parseGOA: parseGOA

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

parseGOA

Description

parse goa_human.gaf

Usage

parseGOA(goa)

Arguments

goa	character string path name to downloaded goa_human.gaf

Details

download goa_human.gaf from https://current.geneontology.org/products/pages/downloads.html

Value

returns matrix with columns c("HGNC","GO","RELATION")

Examples

## Not run: 
# replace my path name for goa with your own!!
# this was obtained from the download sites listed in 'details' section
GOA<-parseGOA("~/goa_human.gaf")
# GOA[1:5,]
#      HGNC          GO           RELATION     
# [1,] "NUDT4B"      "GO:0003723" "enables"    
# [2,] "NUDT4B"      "GO:0005515" "enables"    
# [3,] "NUDT4B"      "GO:0046872" "enables"    
# [4,] "NUDT4B"      "GO:0005829" "located_in" 
# [5,] "TRBV20OR9-2" "GO:0002376" "involved_in"

## End(Not run)
# here is a small example that you can run
f<-system.file("extdata","goa_human.small.gaf",package="minimalistGODB")
GOAsmall<-parseGOA(f)

minimalistGODB documentation built on April 3, 2025, 7:35 p.m.