R/getREACTOMEPATHList.R

In GeneAnswers: Integrated Interpretation of Genes

`getREACTOMEPATHList` <- 
function(geneVector) {
	require(reactome.db)
	if (is.vector(geneVector)) {
		pathIDs <- unique(unlist(lookUp(as.character(geneVector), 'reactome', 'EXTID2PATHID')))
		pathIDs <- pathIDs[!is.na(pathIDs)]
		if (length(pathIDs) > 0) return(lookUp(pathIDs, 'reactome', 'PATHID2EXTID'))
		else return(NULL)
	} else {
		stop('The input is not a vector. Abort GeneAnswers Building ...')
	}
	
	
#	libname <- sub('\\.db', '', lib)
#	idType <- switch(sub('org.*[:.:]', '', libname), 'eg'='EG', 'tair'='TAIR', 'ORF')
#	require(biomaRt)
#	if ("REACTOME" %in% toupper(listMarts()[,'biomart'])) {
#		mart <- useMart("REACTOME")
#		datasets <- listDatasets(mart)
#		pathway<-useDataset("pathway",mart)
#		if (idType == 'EG') {
#			returnType <- c("pathway_db_id", "referencedatabase_entrez_gene")
#			queryType <- 'referencednasequence_entrez_id_list'
#		} else {
#			if (idType == 'TAIR') {
#				returnType <- c("pathway_db_id", "referencedatabase_tigr")
#				queryType <- 'referencepeptidesequence_tigr_id_list'
#			}
#			else stop('ORF is not currently supported by biomaRt!')
#		}
#		print('Start to query biomaRt to retrieve related pathways ...')
#		paths <- unique(as.matrix(getBM(attributes=returnType, filters=queryType, values=geneVector, mart=pathway))[,'pathway_db_id'])
#		print('Start to query biomaRt to retrieve all genes for the related pathways ...')
#		temp <- getBM(attributes=returnType, filters='pathway_db_id_list', values=paths, mart=pathway)
#		return(lapply(.matrix2list(as.matrix(temp[!is.na(temp[,returnType[2]]),]), verbose=FALSE), as.character))
#	} else {
#		stop('REACTOME service is currently not available! Please try later. Abort GeneAnswers Building ...')
#	}
}