R/getREACTOMEPATHTerms.R

In GeneAnswers: Integrated Interpretation of Genes

`getREACTOMEPATHTerms` <- 
function(pathIDs, allowNA=TRUE) {
	if (length(pathIDs) == 0) return(NULL)
	require(reactome.db)
	#pathIDs <- gsub('[^\\d]', '', pathIDs, perl=TRUE)
	# merge the function name from different species
	pathName <- lapply(lookUp(pathIDs, 'reactome', 'PATHID2NAME'), function(x) return(paste(unique(sapply(strsplit(x, ': '), function(y) y[2])), collapse='|'))) 
	if (allowNA) return(pathName[pathIDs])
	else {
		temp <- pathName[pathIDs]
		if (length(temp[which(!is.na(temp))]) > 0) return(temp[which(!is.na(temp))])
		else return(NULL)
	}
#	if (length(pathDBIDs) == 0) return(NULL)
#	require(biomaRt)
#	if ("REACTOME" %in% toupper(listMarts()[,'biomart']))  {
#		mart <- useMart("REACTOME")
#		datasets <- listDatasets(mart)
#		pathway<-useDataset("pathway",mart)
#		returnTable <- getBM(attributes=c('pathway_db_id', '_displayname'), filters='pathway_db_id_list', values=pathDBIDs, mart=pathway)
#		pathName <- .matrix2list(matrix(c(returnTable[,'pathway_db_id'], returnTable[,'_displayname']), ncol=dim(returnTable)[2], dimnames=list(c(1:dim(returnTable)[1]), colnames(returnTable))), verbose=FALSE)
#		if (allowNA) {
#			legalStr <- sapply(pathName, nchar, allowNA=allowNA)
#			return(c(lapply(pathName[which(is.na(legalStr))], function(x) return("The name of this pathway contains special characters and is replaced!")), pathName[which(!is.na(legalStr))])[pathDBIDs]) 
#		} else {
#			print("If you see a warning like : input string  is invalid in this locale, that means names of pathways might contain special characters!") 
#			return(pathName[pathDBIDs])
#		}
#		
#	} else {
#		stop('REACTOME service is currently not available! Please try later.') 
#	}
	
}