R/CNA.EXTS.R

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

setMethodS3("segmentByCBS", "CNA", function(y, ...) {
  # To please R CMD check
  cnData <- y

  # Extract signals of interest
  chromosome <- cnData$chrom
  x <- cnData$maploc
  y <- cnData[,3]
  signalType <- attr(cnData, "data.type")
  sampleName <- colnames(cnData)[3]

# str(list(y=y, chromosome=chromosome, x=x))

  fit <- segmentByCBS(y=y, chromosome=chromosome, x=x, ...)
  sampleName(fit) <- sampleName

  fit
}) # segmentByCBS()