R/gc-effect.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

ezGcEffect = function(rawData, param){
  if (is.null(rawData$signal)){
    rawData$signal = ezNorm(rawData$counts, presentFlag=rawData$presentFlag,  method=param$normMethod)
  }
  isPresent = rowMeans(rawData$presentFlag) >= 0.5
  logSig = log2(rawData$signal + param$backgroundExpression)
  logRatio = logSig - rowMeans(logSig)
  isHighGc = rawData$seqAnno$gc > 0.6 & isPresent
  isLowGc = rawData$seqAnno$gc < 0.4 & isPresent
  gcEffect = apply(logRatio, 2, function(x){mean(x[isHighGc], na.rm = TRUE) - mean(x[isLowGc] ,na.rm = TRUE)})
  return(gcEffect)
}