R/PolarSnpData.R

In aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

setConstructorS3("PolarSnpData", function(data=NULL, ...) {
  if (!is.null(data))
    colnames(data) <- c("radius", "azimuth")
  extend(SnpData(data, ...), "PolarSnpData")
})


setMethodS3("plot", "PolarSnpData", function(x, xlim=NULL, ylim=c(0,pi/2), ...) {
  NextMethod("plot", xlim=xlim, ylim=ylim)
})


setMethodS3("asPolarSnpData", "PolarSnpData", function(this, ...) {
  this
})

setMethodS3("asCartesianSnpData", "PolarSnpData", function(this, ...) {
  polar <- this

  theta <- this
  theta[,1] <- polar[,1] * cos(polar[,2])
  theta[,2] <- polar[,1] * sin(polar[,2])

  CartesianSnpData(theta, ...)
})


setMethodS3("asTotalFracBSnpData", "PolarSnpData", function(this, ...) {
  theta <- asCartesianSnpData(this)
  asTotalFracBSnpData(theta, ...)
})


setMethodS3("pairedBoost", "PolarSnpData", function(this, dataN, ...) {
  # Coerce normal SNP signals
  polarN <- asPolarSnpData(dataN)

  # Assert compatibility
  if (!identical(dim(this), dim(polarN))) {
    throw("Argument 'dataN' is of a non-compatible dimension.")
  }

  # Call normal genotypes
  polarNC <- callGenotypes(polarN, ...)

  # Estimate beta correction factors
  delta <- polarN[,2]-polarNC[,2]

  # Calibrate accordingly
  res <- this
  res[,2] <- res[,2] - delta
  
  res
})