R/RawGenotypeCalls.R

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

setConstructorS3("RawGenotypeCalls", function(...) {
  extend(RawAlleleBFractions(...), "RawGenotypeCalls")
})

setMethodS3("getCalls", "RawGenotypeCalls", function(this, flavor=c("fracB", "AB"), ...) {
  # Argument 'flavor':
  flavor <- match.arg(flavor)

  y <- getSignals(this)
  if (flavor == "fracB") {
    calls <- y
  } else if (flavor == "AB") {
    naValue <- NA_character_
    calls <- rep(naValue, times=nbrOfLoci(this))
    calls[y == 0] <- "AA"
    calls[y == 1/2] <- "AB"
    calls[y == 1] <- "BB"
  }
  calls
})

setMethodS3("isHeterozygous", "RawGenotypeCalls", function(this, ...) {
  calls <- getCalls(this, flavor="fracB", ...)
  res <- (is.finite(calls) & (calls == 1/2))
  res
})

setMethodS3("isHomozygous", "RawGenotypeCalls", function(this, ...) {
  calls <- getCalls(this, flavor="fracB", ...)
  res <- (is.finite(calls) & (calls != 1/2))
  res
})

setMethodS3("getColors", "RawGenotypeCalls", function(this, colorMap=c(AA="red", AB="black", BB="red", "NA"="#999999"), ...) {
  # Argument 'colorMap':
  colorMap <- Arguments$getCharacters(colorMap, useNames=TRUE)
  calls <- getCalls(this, flavor="AB")
  col <- colorMap[calls]
  col[is.na(col)] <- colorMap["NA"]
  col
})