Nothing
`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.')
# }
}
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