R/findAnnotationProbes.R

In wateRmelon: Illumina 450 methylation array normalization and metrics

findAnnotationProbes <-
function(annotationValue, annotations, uniqueAnnot=TRUE){

	temp <- function(x){
		if(uniqueAnnot){
			res <- unique(as.vector(unlist(strsplit(x, split=";"))))
			if(length(res)>1) return("multipleAnnot")
			if(length(res)==1) return(res)
			if(length(res)==0) return(NA)
		}
		else{return(as.vector(unlist(strsplit(x, split=";")))[1])}
	}

	searchList <- apply(as.matrix(annotations[,2]), 1, temp)

	indexNA <- which(is.na(searchList))

	if(length(indexNA)>0) searchList[indexNA] <- "NA"

	if(length(searchList) != dim(annotations)[1]) {
		print("WARNING: in 'findAnnotationProbes.R' search list for annotation probes identification do not have same length than annotations")
	}

	indexProbes <- which(searchList == annotationValue)
	
	if(length(indexProbes)>0) probes <- annotations[indexProbes,1]
	else{print(paste("WARNING: no probes associated to annotation category:", annotationValue, sep="")) ; probes <- NULL}

	return(probes)
}