R/getMULTIANNOTATION.R

In alexandremkuhn/annotationTools: Annotate microarrays and perform cross-species gene expression analyses using flat file databases

getMULTIANNOTATION<-function(identifier,annot,diagnose=FALSE,identifierCol=19,annotationCol=1,noAnnotationSymbol=NA,noAnnotationProvidedSymbol='---') {

	if (is.na(noAnnotationProvidedSymbol)) stop('Argument noAnnotationProvidedSymbol should be different from NA')
	if (!(is.na(noAnnotationSymbol))) {if (noAnnotationSymbol==noAnnotationProvidedSymbol) stop('Argument noAnnotationSymbol and noAnnotationProvidedSymbol should be different')}

	empty<-(is.na(identifier) | identifier=='')
	if (sum(empty)>0) warning('one or more empty ID in input')

	if (sum(empty)==length(empty)) {ps<-as.list(rep(NA,length(empty))); noentry<-rep(FALSE,length(empty)); nops<-rep(FALSE,length(empty))}
	else {
		annotation<-as.list(rep(noAnnotationSymbol,length(identifier)))

		ind<-which(!empty)
		for (i in 1:sum(!empty)) {
			annotation[[ind[i]]]<-annot[which(annot[,identifierCol]==identifier[ind[i]]),annotationCol]
		}

		annotationnb<-sapply(annotation,function(x) {length(x)})
		noentry<-annotationnb==0
		if (sum(noentry)>0) warning('one or more ID not found in annotation')

		noannotation<-annotation==noAnnotationProvidedSymbol
		if (sum(noannotation)>0) warning('One or more ID with no annotation provided in annotation')

		annotation[noentry | noannotation]<-noAnnotationSymbol
	}
	if (diagnose) list(annotation,empty,noentry,noannotation)
	else annotation

}