joinGO: joinGO

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

joinGO

Description

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

Usage

joinGO(GOA, GO)

Arguments

GOA	output of parseGOA()
GO	output of parseGOBASIC()

Value

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

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]

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