R/supportedOrganisms.R

In csdaw/goseq2: Gene Ontology analyser for RNA-seq and other length biased data

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#Description: Lists which genomes and gene IDs are supported by goseq (length and GO terms)
#Notes:
#Author: Nadia Davidson
#Date Modified: 2016/10/04

supportedOrganisms=function(){
   require("rtracklayer")

   #Start by getting the geneLenDataBase supported genomes and geneIDs
   geneIDs=supportedGeneIDs()

   #The names of the supported geneIDs is hard-coded so we can remove things like 
   #"refGene" which actually correspond to an Entrez gene ID in geneLenDataBase
   uniqueIDs=c("knownGene","vegaGene","ensGene","geneSymbol")

   geneIDs=geneIDs[geneIDs$tablename %in% uniqueIDs,]
   
   #extract the corresponding genome IDs and rearrange
   genomes=strsplit(geneIDs$AvailableGenomes,",")
   id=rep(geneIDs$tablename,sapply(genomes,length))
   description=(rep(geneIDs$GeneID,sapply(genomes,length)))
   length_supported=rep(TRUE,length(id))
   genomes=unlist(genomes)
   tab_temp=data.frame(genomes,id,description,length_supported)

   ## Is there GO annotation package for that genome and gene ID?
   genome_supported_go=gsub("[0-9]+","",genomes) %in% names(.ORG_PACKAGES)
   id_supported_go=id %in% names(.ID_MAP)

   go_supported=genome_supported_go & id_supported_go
   tab_temp=data.frame(tab_temp,go_supported)
   colnames(tab_temp)<-c("Genome","Id","Id Description","Lengths in geneLeneDataBase",
   				"GO Annotation Available")   

   ### Add in the newer genomes which aren't supported for length, but are for GO terms
   base=unfactor(ucscGenomes())$db
   other_genomes = base[ ! base %in% genomes ]
   new_genomes=other_genomes[gsub("[0-9]+","",other_genomes) %in% names(.ORG_PACKAGES)]
   new_genomes=c(new_genomes,names(.ORG_PACKAGES)[!names(.ORG_PACKAGES) %in% gsub("[0-9]+","",c(new_genomes,genomes))])
   tab_new=data.frame(new_genomes,"","",FALSE,TRUE)
   colnames(tab_new)<-c("Genome","Id","Id Description","Lengths in geneLeneDataBase",
   				"GO Annotation Available")
   tab_supported=rbind(tab_temp,tab_new)
   tab_supported[order(tab_supported$Genome),]
}