R/ExpressionSetIllumina_calculateDetection.R

In beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

calculateDetection = function(BSData, status=fData(BSData)$Status, negativeLabel="negative"){
  
  detScores = matrix(nrow=nrow(exprs(BSData)),ncol=ncol(exprs(BSData)))
  
  ##Use the fData to find which the negative IDS are 
  
  negInd = which(status == negativeLabel)
  
  
  detect= function(x) 1 - (sum(x>negvals)/(length(negvals)))
  
  pb <- txtProgressBar(min=1,max=ncol(exprs(BSData)),style=3)
  
  
  for(i in 1:ncol(exprs(BSData))){
    
    negvals = exprs(BSData)[negInd,i]
    
    M = median(negvals, na.rm=TRUE)
    MAD = mad(negvals, na.rm=TRUE)
    
    negvals = negvals[negvals < M+3*MAD]
    negvals = negvals[!is.na(negvals)]
    
    detScores[,i] = sapply(exprs(BSData)[,i], detect)
    setTxtProgressBar(pb, i)
    
  }
  
  colnames(detScores) =sampleNames(BSData)
  rownames(detScores) = featureNames(BSData)
  
  
  detScores
  
}