Nothing
##This function creates gene set collections based on GO terms. It is
##species-specific, and returns a GeneSetCollection objects with the
##elements of the gene sets represented by Entrez Gene IDs.
GOGeneSets <- function(species = "Dm", ontologies = "MF") {
##check arguments
paraCheck("species", species)
paraCheck("ontologies", ontologies)
##This creates a list with an element for each GO term, containing
##the Entrez Gene identifiers and corresponding evidence codes
# if(species == "Hs")
# ThisGO<-org.Hs.egGO2EG
# else if(species == "Mm")
# ThisGO<-org.Mm.egGO2EG
# else if(species == "Rn")
# ThisGO<-org.Rn.egGo2EG
# else if(species == "Dm")
# ThisGO<-org.Dm.egGO2EG
# else if(species == "Ce")
# ThisGO<-org.Ce.egGO2EG
annopc<-paste("org", species, "eg", "db", sep=".")
annodb<-paste("org", species, "egGO2EG", sep=".")
ThisGO<-tryCatch(get(annodb), error=function(e) NULL)
if(is.null(ThisGO))
stop(paste('Please load library ', annopc,
' before running this function!', sep=""))
##all GO terms
# all.go.id <- GOID(GOTERM)
GOTERM <- tryCatch(get("GOTERM"), error=function(e) NULL)
if(is.null(GOTERM))
stop(paste('Please load library ', 'GO.db',
' before running this function!', sep=""))
all.go.id <- GOID(GOTERM)
names(all.go.id) <- NULL
##all GO types
all.go.ontology <- Ontology(GOTERM)
##GO terms of species 'species'
this.go.list <- as.list(ThisGO)
##find unique genes of each GO term
this.go.list <- lapply(this.go.list, unique)
this.go.id <- names(this.go.list)
this.go.len <- length(this.go.id)
junk <- sapply(1:this.go.len,
function(s) names(this.go.list[[s]]) <<- NULL)
##tag all GO terms of types in 'ontologies'
this.go.ontology.tag <- rep(FALSE, this.go.len)
this.go.ontology.id <- unlist(sapply(1:length(ontologies),
function(n) {
match.id <- match(this.go.id, all.go.id)
which(all.go.ontology[match.id] == ontologies[n])
}))
this.go.ontology.tag[this.go.ontology.id] <- TRUE
this.go.list <- this.go.list[which(this.go.ontology.tag)]
return(this.go.list)
}
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