R/getControlData.R

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

`getControlData` <-
function(x, type=c('data.frame', 'LumiBatch'), ...) 
{
	type <- match.arg(type)
	if (is.character(x)) {
		if (type == 'data.frame') {
			if ('columnNameGrepPattern' %in% names(list(...))) {
				allControlInfo <- lumiR.batch(x, lib.mapping=NULL, checkDupId=FALSE, convertNuID=FALSE, QC=FALSE, annotationColumn=NULL, ...)
			} else {
				allControlInfo <- lumiR.batch(x, lib.mapping=NULL, checkDupId=FALSE, convertNuID=FALSE, 
					columnNameGrepPattern = list(exprs='AVG_SIGNAL', se.exprs=NA, detection=NA, beadNum=NA), QC=FALSE, annotationColumn=NULL, ...)				
			}
		} else {
			allControlInfo <- lumiR.batch(x, lib.mapping=NULL, checkDupId=FALSE, convertNuID=FALSE, QC=FALSE, annotationColumn=NULL, ...)
			return(allControlInfo)
		}
		x <- allControlInfo
	} 

	if (is(x, 'ExpressionSet')) {
		if (type == 'LumiBatch') {
			return(x)
		} else {
			if (.hasSlot(x, 'controlData')) {
				return(controlData(x))
			} 
			controlData <- as.data.frame(exprs(x))
			controlType <- pData(featureData(x))[,'TargetID']
			ProbeID <- pData(featureData(x))$ProbeID
			if (length(which(toupper(controlType) == 'NEGATIVE')) > 10) {
				controlNames <- names(controlData)
				controlData <- data.frame(controlType=as.character(controlType), ProbeID=as.character(ProbeID), controlData, stringsAsFactors=FALSE)
				names(controlData) <- c('controlType', 'ProbeID', controlNames)
			} else {
				stop("Can't find controlData slot, nor do the TargetID looks like control probes")
			}
		}		
	} else {
		stop('Input data should be a control data file or a LumiBatch object!')
	}
	return(controlData)
}