R/readCfhUnits.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

setMethodS3("readCfhUnits", "default", function(pathname, snps=NULL, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'pathname':
  pathname <- Arguments$getReadablePathname(pathname, mustExist=TRUE)

  # Argument 'units':
  if (!is.null(snps))
    snps <- Arguments$getIndices(snps)

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)


  verbose && enter(verbose, "Reading data from CFH file")
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Retrieve file header
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  hdr <- readCfhHeader(pathname)
  verbose && cat(verbose, "Header:")
  verbose && str(verbose, hdr)
  nbrOfBytes <- hdr$nbrOfBytes
  nbrOfSnps <- hdr$nbrOfSnps
  bytesPerSnp <- hdr$bytesPerSnp

  # Validating units
  if (!is.null(snps))
    snps <- Arguments$getIndices(snps, max=nbrOfSnps)

  map <- matrix(1:(bytesPerSnp*nbrOfSnps), nrow=bytesPerSnp)
  map <- map + hdr$dataOffset

  # Read subset of SNPs?
  if (!is.null(snps))
    map <- map[,snps,drop=FALSE]
  

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Retrieve data
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Read all data
  raw <- readBin(pathname, what=raw(), n=nbrOfBytes)

  # Bytes 1:8 contains (thetaA,thetaB) as floats
  rr <- c(1:8,10:13)
  ncol <- length(rr) / 4
  verbose && cat(verbose, "Number of integers: ", ncol)

  map <- map[rr,,drop=FALSE]
  theta <- readBin(raw[map], what=double(), size=4, endian="little", 
                                                           n=ncol*ncol(map))
  theta <- matrix(theta, ncol=ncol, byrow=TRUE)

#  colnames(theta) <- c("A", "B")

  verbose && exit(verbose)
  
  theta
})