minimalistGODB (version 1.0)

joinGO: joinGO

Description

join the outputs of parseGOA and parseGOBASIC to add the GO category name and the ontology to GOA

Usage

joinGO(GOA, GO)

Value

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

Arguments

GOA

output of parseGOA()

GO

output of parseGOBASIC()

Examples

GOGOA<-joinGO(GOA,GO)
# 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"
# v[5,] "TRBV20OR9-2" "GO:0002376" "involved_in" "immune system process" "biological_process"
# GO_NAME                              
# [1,] "GO_0003723__RNA_binding"          
# [2,] "GO_0005515__protein_binding"      
# [3,] "GO_0046872__metal_ion_binding"    
# [4,] "GO_0005829__cytosol"              
# [5,] "GO_0002376__immune_system_process"

# querying GOGOA to compute gene enrichment of some GO categories
hgncList<-GOGOA[1:1000,"HGNC"]
ontology<-"biological_process"
w<-which(GOGOA[,"ONTOLOGY"] == ontology)
GOGOA<-GOGOA[w,]
w<-which(GOGOA[,"HGNC"] %in% hgncList)
t<-sort(table(GOGOA[w,"NAME"]),decreasing=TRUE)[1:10]