Nothing
R/minimalistGODB.R
In minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB)
Defines functions
grepList
restrictGOA
subsetGOGOA
joinGO
parseGOBASIC
parseGOA
buildGODatabase
buildGODatabaseDriver
Documented in
buildGODatabase
buildGODatabaseDriver
grepList
joinGO
parseGOA
parseGOBASIC
restrictGOA
subsetGOGOA
#' buildGODatabaseDriver
#'
#' @description driver to build multiple GO databases for many species
#'
#' @param goaDir character string path name to directory containing downloaded goa .gaf files
#' @param gobasic character string path name to downloaded go-basic.obo
#' @param dir character string path name to directory to hold species database subdirectories
#' @param verbose Boolean if TRUE print out some diagnostic info
#'
#' @details
#' download goa .gaf files from https://current.geneontology.org/products/pages/downloads.html
#' download go-basic.obo from https://geneontology.org/docs/download-ontology/
#'
#' @examples
#' \dontrun{
#' # replace my path names for goa and gobasic with your own!!
#' # these were obtained from the download sites listed in 'details' section
#' goaDir<-"/Users/barryzeeberg/Downloads/gaf/"
#' gobasic<-"~/go-basic.obo"
#' buildGODatabaseDriver(goaDir,gobasic,dir="~/personal",verbose=TRUE)
#' }
#'
#' # here is a small example that you can run
#' goaDir<-system.file("extdata",package="minimalistGODB")
#' gobasic<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
#' dir<-tempdir()
#' buildGODatabaseDriver(goaDir,gobasic,dir,verbose=TRUE)
#'
#' @details
#' The output GOGOA3 was saved as an .RData file.
#' This was too large for CRAN.
#' It is available from https://github.com/barryzee/GO/tree/main/databases
#'
#' @return returns GO database with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")
#'
#' @export
buildGODatabaseDriver<-
function(goaDir,gobasic,dir=NULL,verbose=FALSE) {
gafs<-list.files(goaDir,pattern="*.gaf",full.names=TRUE)
for(gaf in gafs)
GOGOA3<-buildGODatabase(gaf,gobasic,dir,verbose)
}
#' buildGODatabase
#'
#' @description driver to build GO database
#'
#' @param goa character string path name to downloaded goa_human.gaf
#' @param gobasic character string path name to downloaded go-basic.obo
#' @param dir character string path name to directory to hold subdirectory GODB_RDATA
#' @param 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
#'
#' @examples
#' \dontrun{
#' # 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"
#' buildGODatabase(goa,gobasic,dir="~/",verbose=TRUE)
#' # > 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")
#' buildGODatabase(f1,f2,verbose=TRUE)
#'
#' @details
#' The output GOGOA was saved as an .RData file.
#' This was too large for CRAN.
#' It is available from https://github.com/barryzee/GO/tree/main/databases
#'
#' @return returns no value but has side effect of saving GOGOA3 to a subdirectory
#'
#' @export
buildGODatabase<-
function(goa,gobasic,dir=NULL,verbose=FALSE) {
GOA<-parseGOA(goa)
if(verbose)
print(c("GOA",length(GOA)))
GO<-parseGOBASIC(gobasic,verbose)
if(verbose)
print(c("GO",length(GO)))
GOGOA<-joinGO(GOA,GO)
GOGOA3<-subsetGOGOA(GOGOA)
species<-strsplit(basename(goa),".gaf",fixed=TRUE)[[1]]
#GOGOA3$species<-basename(goa)
GOGOA3$species<-species
if(!is.null(dir)) {
subd<-sprintf("%s/%s",dir,"GODB_RDATA")
if(!dir.exists(subd))
dir.create(subd)
subd2<-sprintf("%s/%s",subd,species)
if(!dir.exists(subd2))
dir.create(subd2)
save(GOA,file=sprintf("%s/GOA_%s.RData",subd2,species))
save(GO,file=sprintf("%s/GO_%s.RData",subd2,species))
save(GOGOA,file=sprintf("%s/GOGOA_%s.RData",subd2,species))
save(GOGOA3,file=sprintf("%s/GOGOA3_%s.RData",subd2,species))
if(verbose)
print(c("SAVING . . . ",sprintf("%s/GOGOA3_%s.RData",subd2,species)))
}
}
#' parseGOA
#'
#' @description parse goa_human.gaf
#'
#' @param goa character string path name to downloaded goa_human.gaf
#'
#' @details
#' download goa_human.gaf from https://current.geneontology.org/products/pages/downloads.html
#'
#' @examples
#' \dontrun{
#' # 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"
#' }
#' # here is a small example that you can run
#' f<-system.file("extdata","goa_human.small.gaf",package="minimalistGODB")
#' GOAsmall<-parseGOA(f)
#'
#'
#' @return returns matrix with columns c("HGNC","GO","RELATION")
#'
#' @export
parseGOA<-
function(goa) {
#x<-strsplit(grep("^UniProtKB",readLines(goa),value=TRUE),"\t")
#x<-strsplit(grep("^MGI",readLines(goa),value=TRUE),"\t")
#print(grepList(species<-strsplit(basename(goa),".gaf",fixed=TRUE)[[1]]))
#x<-strsplit(grep(grepList(basename(goa)),readLines(goa),value=TRUE),"\t")
species<-strsplit(basename(goa),".gaf",fixed=TRUE)[[1]]
gr<-grepList(species)
#print(c("GREP",species,gr))
x<-strsplit(grep(gr,readLines(goa),value=TRUE),"\t")
lx<-length(x)
m<-matrix(nrow=lx,ncol=3)
colnames(m)<-c("HGNC","GO","RELATION")
for(i in 1:lx) {
m[i,"HGNC"]<-x[[i]][3]
m[i,"GO"]<-x[[i]][5]
m[i,"RELATION"]<-x[[i]][4]
}
return(unique(m))
}
#' parseGOBASIC
#'
#' @description parse go-basic.obo
#'
#' @param gobasic character string path name to downloaded go-basic.obo
#' @param verbose Boolean if TRUE print out some diagnostic info
#'
#' @details
#' download go-basic.obo from https://geneontology.org/docs/download-ontology/
#'
#' @examples
#' \dontrun{
#' # 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$bp[1:5,]
#' # GO NAME ONTOLOGY
#' # GO:0000001 "GO:0000001" "mitochondrion inheritance" "biological_process"
#' # GO:0000002 "GO:0000002" "mitochondrial genome maintenance" "biological_process"
#' # GO:0000011 "GO:0000011" "vacuole inheritance" "biological_process"
#' # GO:0000012 "GO:0000012" "single strand break repair" "biological_process"
#' # GO:0000017 "GO:0000017" "alpha-glucoside transport" "biological_process"
#' }
#'
#' # here is a small example that you can run
#' f<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
#' GOsmall<-parseGOBASIC(f)
#'
#' @return returns a list whose components are c("m", "bp", "mf", "cc")
#'
#' @export
parseGOBASIC<-
function(gobasic,verbose=FALSE) {
l<-list()
x<-readLines(gobasic)
v<-grep("[Term]",x,fixed=TRUE)
lv<-length(v)
if(verbose)
message(c("number of terms:",lv))
m<-matrix(nrow=lv,ncol=3)
colnames(m)<-c("GO","NAME","ONTOLOGY")
for(i in 1:lv) {
m[i,"GO"]<-x[v[i]+1]
m[i,"NAME"]<-x[v[i]+2]
m[i,"ONTOLOGY"]<-x[v[i]+3]
}
if(verbose) {
message(c("initial m"))
message(m[1:3,])
}
# filter out "obsolete" in "NAME"
g<-grep("obsolete",m[,"NAME"])
if(length(g)>0)
m<-m[-g,]
if(verbose) {
message(c("non obsolete m"))
message(m[1:3,])
}
m[,"GO"]<-substring(m[,"GO"],5,14)
m[,"NAME"]<-substring(m[,"NAME"],7,1000)
m[,"ONTOLOGY"]<-substring(m[,"ONTOLOGY"],12,50)
rownames(m)<-m[,"GO"]
bp<-grep("biological_process",m[,"ONTOLOGY"])
if(verbose) {
message(c("BP indices",length(bp)))
message(bp[1:10])
message(m[bp[1:10],])
}
l$m<-m
l$bp<-m[bp,]
mf<-grep("molecular_function",m[,"ONTOLOGY"])
l$mf<-m[mf,]
cc<-grep("cellular_component",m[,"ONTOLOGY"])
l$cc<-m[cc,]
# https://geneontology.org/stats.html
if(verbose) {
message("THEORETICAL NUMBER OF TERMS 26091 10154 4022")
lx<-length(x)
message(c("LX",lx,"LBP",length(bp),"LMF",length(mf),"LCC",length(cc)))
}
return(l)
}
#' joinGO
#'
#' @description join the outputs of parseGOA and parseGOBASIC to add the GO category name and the ontology to GOA
#'
#' @param GOA output of parseGOA()
#' @param GO output of parseGOBASIC()
#'
#' @examples
#' GOGOA<-joinGO(GOA,GO)
#' # GOGOA[1:5,]
#' # HGNC GO RELATION NAME ONTOLOGY
#' # [1,] "NUDT4B" "GO:0003723" "enables" "RNA binding" "molecular_function"
#' # [2,] "NUDT4B" "GO:0005515" "enables" "protein binding" "molecular_function"
#' # [3,] "NUDT4B" "GO:0046872" "enables" "metal ion binding" "molecular_function"
#' # [4,] "NUDT4B" "GO:0005829" "located_in" "cytosol" "cellular_component"
#' # v[5,] "TRBV20OR9-2" "GO:0002376" "involved_in" "immune system process" "biological_process"
#' # GO_NAME
#' # [1,] "GO_0003723__RNA_binding"
#' # [2,] "GO_0005515__protein_binding"
#' # [3,] "GO_0046872__metal_ion_binding"
#' # [4,] "GO_0005829__cytosol"
#' # [5,] "GO_0002376__immune_system_process"
#'
#' # querying GOGOA to compute gene enrichment of some GO categories
#' hgncList<-GOGOA[1:1000,"HGNC"]
#' ontology<-"biological_process"
#' w<-which(GOGOA[,"ONTOLOGY"] == ontology)
#' GOGOA<-GOGOA[w,]
#' w<-which(GOGOA[,"HGNC"] %in% hgncList)
#' t<-sort(table(GOGOA[w,"NAME"]),decreasing=TRUE)[1:10]
#'
#' @return returns a matrix with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")
#'
#' @export
joinGO<-
function(GOA,GO) {
#m<-matrix(nrow=nrow(GOA),ncol=5)
# restrict GO categories in GOA to those in GO
GOA<-restrictGOA(GOA,GO)
NAME<-GO$m[GOA[,"GO"],"NAME"]
gx<-cbind(GOA,NAME)
rownames(gx)<-NULL
ONTOLOGY<-GO$m[GOA[,"GO"],"ONTOLOGY"]
gxx<-cbind(gx,ONTOLOGY)
rownames(gxx)<-NULL
# generate 'safe' (suitable to be used as a variable or file name) combined GO category name
#GO_NAME<-sprintf("%s__%s",gsub(":","_",gxx[,"GO"]),gsub(" ","_",gxx[,"NAME"]))
GO_NAME<-sprintf("%s__%s",gsub(":","_",gxx[,"GO"]),gsub("[ /,]","_",gxx[,"NAME"]))
gxxx<-cbind(gxx,GO_NAME)
return(gxxx)
}
#' subsetGOGOA
#'
#' @description split GOGOA into 3 separate ontologies
#'
#' @param GOGOA return value of minimalistGODB::joinGO()
#'
#' @examples
#' #load("data/GOGOAsmall.RData")
#' GOGOA3small<-subsetGOGOA(GOGOAsmall)
#'
#' @return returns a list containing subsets of GOGOA for each ontology, unique gene and cat lists, and stats
#'
#' @export
subsetGOGOA<-
function(GOGOA) {
l<-list()
l$ontologies<-list()
ontologies<-unique(GOGOA[,"ONTOLOGY"])
for(ONTOLOGY in ontologies) {
w<-which(GOGOA[,"ONTOLOGY"] == ONTOLOGY)
l$ontologies[[ONTOLOGY]]<-as.matrix(GOGOA[w,c("HGNC","GO","RELATION","NAME","GO_NAME")])
}
l$cats<-list()
l$genes<-list()
l$stats<-list()
l$stats$ncats<-list()
l$stats$ngenes<-list()
for(ONTOLOGY in ontologies) {
l$cats[[ONTOLOGY]]<-unique(l$ontologies[[ONTOLOGY]][,"GO_NAME"])
l$stats$ncats[[ONTOLOGY]]<-length(l$cats[[ONTOLOGY]])
l$genes[[ONTOLOGY]]<-unique(l$ontologies[[ONTOLOGY]][,"HGNC"])
l$stats$ngenes[[ONTOLOGY]]<-length(l$genes[[ONTOLOGY]])
ngenes<-as.matrix(sort(table(l$ontologies[[ONTOLOGY]][,"GO_NAME"]),decreasing=TRUE))
fgenes<-ngenes/l$stats$ngenes[[ONTOLOGY]]
l$stats$tcats[[ONTOLOGY]]<-cbind(ngenes,fgenes)
}
l$genes[["ALL"]]<-unique(GOGOA[,"HGNC"])
l$cats[["ALL"]]<-unique(GOGOA[,"GO_NAME"])
return(l)
}
#' restrictGOA
#'
#' @description restrict GO categories in GOA to those in GO
#'
#' @param GOA output of parseGOA()
#' @param GO output of parseGOBASIC()
#'
#' @examples
#' GOA<-restrictGOA(GOA,GO)
#'
#' @return returns a restricted version of GOA
#'
#' @export
restrictGOA<-
function(GOA,GO) {
good<-intersect(unique(rownames(GO$m)),unique(GOA[,"GO"]))
w<-which(GOA[,"GO"] %in% good)
return(GOA[w,])
}
#' grepList
#'
#' @description determine the correct pattern to grep for depending on the species
#'
#' @param gaf character string containing the basename of the gaf file downloaded
#' from https://current.geneontology.org/products/pages/downloads.html
#'
#' @examples
#' pattern<-grepList("tair.gaf")
#'
#' @return returns the correct pattern to grep for
#'
#' @export
grepList<-
function(gaf) {
v<-vector("character")
v["cgd"]<-"^CGD"
v["dictybase"]<-"^dictyBase"
v["ecocyc"]<-"^UniProtKB"
v["fb"]<-"^FB"
v["genedb_lmajor"]<-"^TriTrypDB"
v["genedb_pfalciparum"]<-"^PlasmoDB"
v["genedb_tbrucei"]<-"^TriTrypDB"
v["goa_chicken"]<-"^UniProtKB"
v["goa_cow"]<-"^UniProtKB"
v["goa_dog"]<-"^UniProtKB"
v["goa_human"]<-"^UniProtKB"
v["goa_pig"]<-"^UniProtKB"
v["japonicusdb"]<-"^JaponicusDB"
v["mgi"]<-"^MGI"
v["pombase"]<-"^PomBase"
v["pseudocap"]<-"^PseudoCAP"
# v["reactome"]<-"^"
v["rgd"]<-"^RGD"
v["sgd"]<-"^SGD"
v["sgn"]<-"^SGN"
v["tair"]<-"^AGI_LocusCode"
v["wb"]<-"^WB"
v["xenbase"]<-"^Xenbase"
v["zfin"]<-"^ZFIN"
return(v[gaf])
}
Try the minimalistGODB package in your browser
Any scripts or data that you put into this service are public.
minimalistGODB documentation built on June 8, 2025, 11:41 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions grepList restrictGOA subsetGOGOA joinGO parseGOBASIC parseGOA buildGODatabase buildGODatabaseDriver
Documented in buildGODatabase buildGODatabaseDriver grepList joinGO parseGOA parseGOBASIC restrictGOA subsetGOGOA
#' buildGODatabaseDriver
#'
#' @description driver to build multiple GO databases for many species
#'
#' @param goaDir character string path name to directory containing downloaded goa .gaf files
#' @param gobasic character string path name to downloaded go-basic.obo
#' @param dir character string path name to directory to hold species database subdirectories
#' @param verbose Boolean if TRUE print out some diagnostic info
#'
#' @details
#' download goa .gaf files from https://current.geneontology.org/products/pages/downloads.html
#' download go-basic.obo from https://geneontology.org/docs/download-ontology/
#'
#' @examples
#' \dontrun{
#' # replace my path names for goa and gobasic with your own!!
#' # these were obtained from the download sites listed in 'details' section
#' goaDir<-"/Users/barryzeeberg/Downloads/gaf/"
#' gobasic<-"~/go-basic.obo"
#' buildGODatabaseDriver(goaDir,gobasic,dir="~/personal",verbose=TRUE)
#' }
#'
#' # here is a small example that you can run
#' goaDir<-system.file("extdata",package="minimalistGODB")
#' gobasic<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
#' dir<-tempdir()
#' buildGODatabaseDriver(goaDir,gobasic,dir,verbose=TRUE)
#'
#' @details
#' The output GOGOA3 was saved as an .RData file.
#' This was too large for CRAN.
#' It is available from https://github.com/barryzee/GO/tree/main/databases
#'
#' @return returns GO database with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")
#'
#' @export
buildGODatabaseDriver<-
function(goaDir,gobasic,dir=NULL,verbose=FALSE) {
gafs<-list.files(goaDir,pattern="*.gaf",full.names=TRUE)
for(gaf in gafs)
GOGOA3<-buildGODatabase(gaf,gobasic,dir,verbose)
}
#' buildGODatabase
#'
#' @description driver to build GO database
#'
#' @param goa character string path name to downloaded goa_human.gaf
#' @param gobasic character string path name to downloaded go-basic.obo
#' @param dir character string path name to directory to hold subdirectory GODB_RDATA
#' @param 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
#'
#' @examples
#' \dontrun{
#' # 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"
#' buildGODatabase(goa,gobasic,dir="~/",verbose=TRUE)
#' # > 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")
#' buildGODatabase(f1,f2,verbose=TRUE)
#'
#' @details
#' The output GOGOA was saved as an .RData file.
#' This was too large for CRAN.
#' It is available from https://github.com/barryzee/GO/tree/main/databases
#'
#' @return returns no value but has side effect of saving GOGOA3 to a subdirectory
#'
#' @export
buildGODatabase<-
function(goa,gobasic,dir=NULL,verbose=FALSE) {
GOA<-parseGOA(goa)
if(verbose)
print(c("GOA",length(GOA)))
GO<-parseGOBASIC(gobasic,verbose)
if(verbose)
print(c("GO",length(GO)))
GOGOA<-joinGO(GOA,GO)
GOGOA3<-subsetGOGOA(GOGOA)
species<-strsplit(basename(goa),".gaf",fixed=TRUE)[[1]]
#GOGOA3$species<-basename(goa)
GOGOA3$species<-species
if(!is.null(dir)) {
subd<-sprintf("%s/%s",dir,"GODB_RDATA")
if(!dir.exists(subd))
dir.create(subd)
subd2<-sprintf("%s/%s",subd,species)
if(!dir.exists(subd2))
dir.create(subd2)
save(GOA,file=sprintf("%s/GOA_%s.RData",subd2,species))
save(GO,file=sprintf("%s/GO_%s.RData",subd2,species))
save(GOGOA,file=sprintf("%s/GOGOA_%s.RData",subd2,species))
save(GOGOA3,file=sprintf("%s/GOGOA3_%s.RData",subd2,species))
if(verbose)
print(c("SAVING . . . ",sprintf("%s/GOGOA3_%s.RData",subd2,species)))
}
}
#' parseGOA
#'
#' @description parse goa_human.gaf
#'
#' @param goa character string path name to downloaded goa_human.gaf
#'
#' @details
#' download goa_human.gaf from https://current.geneontology.org/products/pages/downloads.html
#'
#' @examples
#' \dontrun{
#' # 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"
#' }
#' # here is a small example that you can run
#' f<-system.file("extdata","goa_human.small.gaf",package="minimalistGODB")
#' GOAsmall<-parseGOA(f)
#'
#'
#' @return returns matrix with columns c("HGNC","GO","RELATION")
#'
#' @export
parseGOA<-
function(goa) {
#x<-strsplit(grep("^UniProtKB",readLines(goa),value=TRUE),"\t")
#x<-strsplit(grep("^MGI",readLines(goa),value=TRUE),"\t")
#print(grepList(species<-strsplit(basename(goa),".gaf",fixed=TRUE)[[1]]))
#x<-strsplit(grep(grepList(basename(goa)),readLines(goa),value=TRUE),"\t")
species<-strsplit(basename(goa),".gaf",fixed=TRUE)[[1]]
gr<-grepList(species)
#print(c("GREP",species,gr))
x<-strsplit(grep(gr,readLines(goa),value=TRUE),"\t")
lx<-length(x)
m<-matrix(nrow=lx,ncol=3)
colnames(m)<-c("HGNC","GO","RELATION")
for(i in 1:lx) {
m[i,"HGNC"]<-x[[i]][3]
m[i,"GO"]<-x[[i]][5]
m[i,"RELATION"]<-x[[i]][4]
}
return(unique(m))
}
#' parseGOBASIC
#'
#' @description parse go-basic.obo
#'
#' @param gobasic character string path name to downloaded go-basic.obo
#' @param verbose Boolean if TRUE print out some diagnostic info
#'
#' @details
#' download go-basic.obo from https://geneontology.org/docs/download-ontology/
#'
#' @examples
#' \dontrun{
#' # 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$bp[1:5,]
#' # GO NAME ONTOLOGY
#' # GO:0000001 "GO:0000001" "mitochondrion inheritance" "biological_process"
#' # GO:0000002 "GO:0000002" "mitochondrial genome maintenance" "biological_process"
#' # GO:0000011 "GO:0000011" "vacuole inheritance" "biological_process"
#' # GO:0000012 "GO:0000012" "single strand break repair" "biological_process"
#' # GO:0000017 "GO:0000017" "alpha-glucoside transport" "biological_process"
#' }
#'
#' # here is a small example that you can run
#' f<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
#' GOsmall<-parseGOBASIC(f)
#'
#' @return returns a list whose components are c("m", "bp", "mf", "cc")
#'
#' @export
parseGOBASIC<-
function(gobasic,verbose=FALSE) {
l<-list()
x<-readLines(gobasic)
v<-grep("[Term]",x,fixed=TRUE)
lv<-length(v)
if(verbose)
message(c("number of terms:",lv))
m<-matrix(nrow=lv,ncol=3)
colnames(m)<-c("GO","NAME","ONTOLOGY")
for(i in 1:lv) {
m[i,"GO"]<-x[v[i]+1]
m[i,"NAME"]<-x[v[i]+2]
m[i,"ONTOLOGY"]<-x[v[i]+3]
}
if(verbose) {
message(c("initial m"))
message(m[1:3,])
}
# filter out "obsolete" in "NAME"
g<-grep("obsolete",m[,"NAME"])
if(length(g)>0)
m<-m[-g,]
if(verbose) {
message(c("non obsolete m"))
message(m[1:3,])
}
m[,"GO"]<-substring(m[,"GO"],5,14)
m[,"NAME"]<-substring(m[,"NAME"],7,1000)
m[,"ONTOLOGY"]<-substring(m[,"ONTOLOGY"],12,50)
rownames(m)<-m[,"GO"]
bp<-grep("biological_process",m[,"ONTOLOGY"])
if(verbose) {
message(c("BP indices",length(bp)))
message(bp[1:10])
message(m[bp[1:10],])
}
l$m<-m
l$bp<-m[bp,]
mf<-grep("molecular_function",m[,"ONTOLOGY"])
l$mf<-m[mf,]
cc<-grep("cellular_component",m[,"ONTOLOGY"])
l$cc<-m[cc,]
# https://geneontology.org/stats.html
if(verbose) {
message("THEORETICAL NUMBER OF TERMS 26091 10154 4022")
lx<-length(x)
message(c("LX",lx,"LBP",length(bp),"LMF",length(mf),"LCC",length(cc)))
}
return(l)
}
#' joinGO
#'
#' @description join the outputs of parseGOA and parseGOBASIC to add the GO category name and the ontology to GOA
#'
#' @param GOA output of parseGOA()
#' @param GO output of parseGOBASIC()
#'
#' @examples
#' GOGOA<-joinGO(GOA,GO)
#' # GOGOA[1:5,]
#' # HGNC GO RELATION NAME ONTOLOGY
#' # [1,] "NUDT4B" "GO:0003723" "enables" "RNA binding" "molecular_function"
#' # [2,] "NUDT4B" "GO:0005515" "enables" "protein binding" "molecular_function"
#' # [3,] "NUDT4B" "GO:0046872" "enables" "metal ion binding" "molecular_function"
#' # [4,] "NUDT4B" "GO:0005829" "located_in" "cytosol" "cellular_component"
#' # v[5,] "TRBV20OR9-2" "GO:0002376" "involved_in" "immune system process" "biological_process"
#' # GO_NAME
#' # [1,] "GO_0003723__RNA_binding"
#' # [2,] "GO_0005515__protein_binding"
#' # [3,] "GO_0046872__metal_ion_binding"
#' # [4,] "GO_0005829__cytosol"
#' # [5,] "GO_0002376__immune_system_process"
#'
#' # querying GOGOA to compute gene enrichment of some GO categories
#' hgncList<-GOGOA[1:1000,"HGNC"]
#' ontology<-"biological_process"
#' w<-which(GOGOA[,"ONTOLOGY"] == ontology)
#' GOGOA<-GOGOA[w,]
#' w<-which(GOGOA[,"HGNC"] %in% hgncList)
#' t<-sort(table(GOGOA[w,"NAME"]),decreasing=TRUE)[1:10]
#'
#' @return returns a matrix with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")
#'
#' @export
joinGO<-
function(GOA,GO) {
#m<-matrix(nrow=nrow(GOA),ncol=5)
# restrict GO categories in GOA to those in GO
GOA<-restrictGOA(GOA,GO)
NAME<-GO$m[GOA[,"GO"],"NAME"]
gx<-cbind(GOA,NAME)
rownames(gx)<-NULL
ONTOLOGY<-GO$m[GOA[,"GO"],"ONTOLOGY"]
gxx<-cbind(gx,ONTOLOGY)
rownames(gxx)<-NULL
# generate 'safe' (suitable to be used as a variable or file name) combined GO category name
#GO_NAME<-sprintf("%s__%s",gsub(":","_",gxx[,"GO"]),gsub(" ","_",gxx[,"NAME"]))
GO_NAME<-sprintf("%s__%s",gsub(":","_",gxx[,"GO"]),gsub("[ /,]","_",gxx[,"NAME"]))
gxxx<-cbind(gxx,GO_NAME)
return(gxxx)
}
#' subsetGOGOA
#'
#' @description split GOGOA into 3 separate ontologies
#'
#' @param GOGOA return value of minimalistGODB::joinGO()
#'
#' @examples
#' #load("data/GOGOAsmall.RData")
#' GOGOA3small<-subsetGOGOA(GOGOAsmall)
#'
#' @return returns a list containing subsets of GOGOA for each ontology, unique gene and cat lists, and stats
#'
#' @export
subsetGOGOA<-
function(GOGOA) {
l<-list()
l$ontologies<-list()
ontologies<-unique(GOGOA[,"ONTOLOGY"])
for(ONTOLOGY in ontologies) {
w<-which(GOGOA[,"ONTOLOGY"] == ONTOLOGY)
l$ontologies[[ONTOLOGY]]<-as.matrix(GOGOA[w,c("HGNC","GO","RELATION","NAME","GO_NAME")])
}
l$cats<-list()
l$genes<-list()
l$stats<-list()
l$stats$ncats<-list()
l$stats$ngenes<-list()
for(ONTOLOGY in ontologies) {
l$cats[[ONTOLOGY]]<-unique(l$ontologies[[ONTOLOGY]][,"GO_NAME"])
l$stats$ncats[[ONTOLOGY]]<-length(l$cats[[ONTOLOGY]])
l$genes[[ONTOLOGY]]<-unique(l$ontologies[[ONTOLOGY]][,"HGNC"])
l$stats$ngenes[[ONTOLOGY]]<-length(l$genes[[ONTOLOGY]])
ngenes<-as.matrix(sort(table(l$ontologies[[ONTOLOGY]][,"GO_NAME"]),decreasing=TRUE))
fgenes<-ngenes/l$stats$ngenes[[ONTOLOGY]]
l$stats$tcats[[ONTOLOGY]]<-cbind(ngenes,fgenes)
}
l$genes[["ALL"]]<-unique(GOGOA[,"HGNC"])
l$cats[["ALL"]]<-unique(GOGOA[,"GO_NAME"])
return(l)
}
#' restrictGOA
#'
#' @description restrict GO categories in GOA to those in GO
#'
#' @param GOA output of parseGOA()
#' @param GO output of parseGOBASIC()
#'
#' @examples
#' GOA<-restrictGOA(GOA,GO)
#'
#' @return returns a restricted version of GOA
#'
#' @export
restrictGOA<-
function(GOA,GO) {
good<-intersect(unique(rownames(GO$m)),unique(GOA[,"GO"]))
w<-which(GOA[,"GO"] %in% good)
return(GOA[w,])
}
#' grepList
#'
#' @description determine the correct pattern to grep for depending on the species
#'
#' @param gaf character string containing the basename of the gaf file downloaded
#' from https://current.geneontology.org/products/pages/downloads.html
#'
#' @examples
#' pattern<-grepList("tair.gaf")
#'
#' @return returns the correct pattern to grep for
#'
#' @export
grepList<-
function(gaf) {
v<-vector("character")
v["cgd"]<-"^CGD"
v["dictybase"]<-"^dictyBase"
v["ecocyc"]<-"^UniProtKB"
v["fb"]<-"^FB"
v["genedb_lmajor"]<-"^TriTrypDB"
v["genedb_pfalciparum"]<-"^PlasmoDB"
v["genedb_tbrucei"]<-"^TriTrypDB"
v["goa_chicken"]<-"^UniProtKB"
v["goa_cow"]<-"^UniProtKB"
v["goa_dog"]<-"^UniProtKB"
v["goa_human"]<-"^UniProtKB"
v["goa_pig"]<-"^UniProtKB"
v["japonicusdb"]<-"^JaponicusDB"
v["mgi"]<-"^MGI"
v["pombase"]<-"^PomBase"
v["pseudocap"]<-"^PseudoCAP"
# v["reactome"]<-"^"
v["rgd"]<-"^RGD"
v["sgd"]<-"^SGD"
v["sgn"]<-"^SGN"
v["tair"]<-"^AGI_LocusCode"
v["wb"]<-"^WB"
v["xenbase"]<-"^Xenbase"
v["zfin"]<-"^ZFIN"
return(v[gaf])
}
Try the minimalistGODB package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.