R/PairedPSCNData.R

In HenrikBengtsson/aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

###########################################################################/**
# @RdocClass PairedPSCNData
#
# @title "The PairedPSCNData class"
#
# \description{
#  @classhierarchy
#
#  A PairedPSCNData object holds paired tumor-normal parent-specific
#  copy number data.
# }
#
# @synopsis
#
# \arguments{
#   \item{CT}{A @numeric @vector of J tumor total copy number (TCN)
#        ratios in [0,+@Inf) (due to noise, small negative values are
#        also allowed).  The TCN ratios are typically scaled such that
#        copy-neutral diploid loci have a mean of two.}
#   \item{CN}{An optional @numeric @vector of J normal TCN ratios.}
#   \item{betaT}{A @numeric @vector of J tumor allele B fractions (BAFs)
#        in [0,1] (due to noise, values may be slightly outside as well)
#        or @NA for non-polymorphic loci.}
#   \item{betaN}{A @numeric @vector of J matched normal BAFs in [0,1]
#        (due to noise, values may be slightly outside as well) or @NA
#        for non-polymorphic loci.}
#   \item{muN}{An optional @numeric @vector of J genotype calls in
#        \{0,1/2,1\} for AA, AB, and BB, respectively,
#        and @NA for non-polymorphic loci.
#        If not given, they are estimated from the normal BAFs using
#        @see "aroma.light::callNaiveGenotypes" as described in [2].}
#   \item{isSNP}{An optional @logical @vector of length J specifying
#        whether each locus is a SNP or not (non-polymorphic loci).}
#   \item{chromosome}{(Optional) An @integer scalar (or a @vector of length J),
#        which can be used to specify which chromosome each locus belongs to
#        in case multiple chromosomes are segments.
#        This argument is also used for annotation purposes.}
#   \item{x}{Optional @numeric @vector of J genomic locations.
#            If @NULL, index locations \code{1:J} are used.}
#   \item{...}{Optional named locus-specific signal @vectors of length J.}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author
#*/###########################################################################
setConstructorS3("PairedPSCNData", function(chromosome=NULL, x=NULL, isSNP=NULL, muN=NULL, CT=NULL, betaT=NULL, CN=NULL, betaN=NULL, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (!is.null(chromosome)) {
    # Is first argument special?
    if (is.data.frame(chromosome)) {
      data <- chromosome

      chromosome <- data$chromosome
      x <- data$x
      isSNP <- data$isSNP
      muN <- data$muN
      CT <- data$CT
      betaT <- data$betaT
      CN <- data$CN
      betaN <- data$betaN
    }

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Required arguments
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Argument 'CT':
    disallow <- c("Inf")
    CT <- Arguments$getDoubles(CT, disallow=disallow)

    nbrOfLoci <- length(CT)
    length2 <- rep(nbrOfLoci, times=2)

    # Argument 'betaT':
    betaT <- Arguments$getDoubles(betaT, length=length2, disallow="Inf")


    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Mutually optional arguments (that are not validated in superclass)
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Argument 'betaN':
    if (!is.null(betaN)) {
      betaN <- Arguments$getDoubles(betaN, length=length2, disallow="Inf")
    }

    if (is.null(betaN) && is.null(muN)) {
      throw("If argument 'betaN' is not given, then 'muN' must be.")
    }


    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Optional arguments
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Argument 'CN':
    if (!is.null(CN)) {
      disallow <- c("Inf")
      CN <- Arguments$getDoubles(CN, length=length2, disallow=disallow)
    }

    # Argument 'chromosome':
    if (is.null(chromosome)) {
      chromosome <- 0L
    } else {
      disallow <- c("Inf")
      chromosome <- Arguments$getIntegers(chromosome, range=c(0,Inf), disallow=disallow)
    }

    if (length(chromosome) == 1) {
      chromosome <- rep(chromosome, times=nbrOfLoci)
    } else {
      chromosome <- Arguments$getIntegers(chromosome, length=length2, disallow=disallow)
    }
  }

##  cat("PairedPSCNData...\n")
  this <- extend(AbstractPSCNData(chromosome=chromosome, x=x, isSNP=isSNP, muN=muN, y=CT, CN=CN, betaT=betaT, betaN=betaN, ...), "PairedPSCNData")
##  cat("PairedPSCNData...done\n")

  this <- setColumnNamesMap(this, y="CT")

  this
})


setMethodS3("as.PairedPSCNData", "PairedPSCNData", function(this, ...) {
  this
})

setMethodS3("as.PairedPSCNData", "data.frame", function(this, ...) {
  data <- this
  PairedPSCNData(data, ...)
})

setMethodS3("as.PairedPSCNData", "NonPairedPSCNData", function(T, N, ..., verbose=FALSE) {
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Merging matched tumor-normal pair of data")
  dataT <- as.data.frame(T)
  dataN <- as.data.frame(N)

  verbose && enter(verbose, "Asserting compatible sets of loci")
  # Compatibility check
  for (key in c("chromosome", "x", "isSNP")) {
    vT <- dataT[[key]]
    vN <- dataN[[key]]
    if (is.null(vT) || is.null(vN)) {
      next
    }
    .stop_if_not(all.equal(vT, vN))
  } # for (key ...)
  verbose && exit(verbose)

  names <- colnames(dataT)
  idxs <- which(is.element(names, c("C", "beta", "mu")))
  names[idxs] <- sprintf("%sT", names[idxs])
  colnames(dataT) <- names

  names <- colnames(dataN)
  idxs <- which(is.element(names, c("C", "beta", "mu")))
  names[idxs] <- sprintf("%sN", names[idxs])
  colnames(dataN) <- names

#  verbose && str(verbose, dataT)
#  verbose && str(verbose, dataN)

  data <- cbind(dataT, dataN)
  names <- colnames(data)
  keep <- !duplicated(names)
  data <- data[,keep,drop=FALSE]
  verbose && str(verbose, data)

  res <- PairedPSCNData(data, ...)

  verbose && print(verbose, res)

  verbose && exit(verbose)

  res
})


setMethodS3("extractNonPairedPSCNData", "PairedPSCNData", function(this, which=c("T", "N"), ..., verbose=FALSE) {
  # Argument 'which':
  which <- match.arg(which)

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Extracting Non-paired PSCN data")

  # Identify fields to keep
  fields0 <- c("chromosome", "x", "isSNP")
  fieldsW <- sprintf("%s%s", c("mu", "C", "beta"), which)
  fields <- c(fields0, fieldsW)

  verbose && cat(verbose, "Columns to extract:")
  verbose && print(verbose, fields)

  # Extract subset of fields
  data <- as.data.frame(this)
  names <- colnames(data)
  keep <- names[is.element(names, fields)]
  data <- data[,keep, drop=FALSE]

  verbose && cat(verbose, "Extracted signals:")
  verbose && str(verbose, data)

  # Rename fields
  names <- colnames(data)
  idxs <- match(fieldsW, names)
  idxs <- na.omit(idxs)
  names[idxs] <- gsub("N$", "", names[idxs])
  colnames(data) <- names

  verbose && cat(verbose, "Extracted renamed signals:")
  verbose && str(verbose, data)

  # Return
  res <- NonPairedPSCNData(data)

  verbose && exit(verbose)

  res
}, protected=TRUE)


setMethodS3("getSignalColumnNames", "PairedPSCNData", function(this, ...) {
  names <- getColumnNames(this, ...)
  names <- grep("^(C|beta|mu|isSNP)", names, value=TRUE)
  names <- unique(c("CT", names))
  names
})


setMethodS3("callNaiveGenotypes", "PairedPSCNData", function(this, force=FALSE, ..., verbose=FALSE) {
  data <- this

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Calling genotypes from normal allele B fractions")

  muN <- data$muN
  if (!force && !is.null(muN)) {
    verbose && cat(verbose, "Already done. Skipping.")
    verbose && exit(verbose)
    return(data)
  }

  verbose && enter(verbose, "Calling genotypes from germline data")
  dataN <- extractNonPairedPSCNData(this, which="N", verbose=less(verbose, 5))
  verbose && print(verbose, data)

  dataN <- callNaiveGenotypes(dataN, ..., verbose=less(verbose, 5))
  muN <- dataN$mu
  verbose && summary(verbose, muN)
  verbose && print(verbose, table(muN))

  # Not needed anymore
  dataN <- NULL
  verbose && exit(verbose)


  data$muN <- muN
  verbose && exit(verbose)

  data
})


setMethodS3("normalizeTumorBoost", "PairedPSCNData", function(this, preserveScale=TRUE, force=FALSE, ..., verbose=FALSE) {
  data <- this

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Normalizing tumor BAFs using normal BAFs (TumorBoost)")

  betaTN <- data$betaTN
  if (!force && !is.null(betaTN)) {
    verbose && cat(verbose, "Already done. Skipping.")
    verbose && exit(verbose)
    return(data)
  }

  betaT <- data$betaT
  betaN <- data$betaN
  muN <- data$muN

  betaTN <- aroma.light::normalizeTumorBoost(betaT=betaT, betaN=betaN, muN=muN, preserveScale=preserveScale)
  verbose && cat(verbose, "Normalized tumor BAFs:")
  verbose && str(verbose, betaTN)

  # Assert that no missing values where introduced
  keep <- (is.finite(betaT) & is.finite(betaN) & is.finite(muN))
  if (any(is.na(betaTN[keep]))) {
    throw("Internal error: normalizeTumorBoost() introduced missing values.")
  }
  # Not needed anymore
  keep <- NULL

  data$betaTN <- betaTN
  verbose && exit(verbose)

  data
}) # normalizeTumorBoost()





setMethodS3("getTotalCopyNumbers", "PairedPSCNData", function(this, what=c("CT", "2*CT/CN"), ...) {
  data <- this

  # Argument 'what':
  what <- match.arg(what)

  CT <- data$CT

  if (what == "2*CT/CN") {
    CN <- data$CN
    CT <- 2*CT/CN
  }

  CT
})

setMethodS3("getTCNs", "PairedPSCNData", function(...) {
  getTotalCopyNumbers(...)
})



setMethodS3("callSegmentationOutliers", "PairedPSCNData", function(y, ..., verbose=FALSE) {
  pkg <- "PSCBS"
  require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)

  # To please R CMD check
  this <- y

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Calling total copy-number segmentation outliers")
  data <- as.data.frame(this)
  verbose && str(verbose, data)

  res <- callSegmentationOutliers(y=data$CT, chromosome=data$chromosome, x=data$x, ..., verbose=less(verbose, 10))

  verbose && str(verbose, res)
  verbose && exit(verbose)

  res
}) # callSegmentationOutliers()


setMethodS3("dropSegmentationOutliers", "PairedPSCNData", function(CT, ...) {
  # To please R CMD check
  this <- CT

  isOutlier <- callSegmentationOutliers(this, ...)

  if (any(isOutlier)) {
    naValue <- NA_real_
    C <- getSignals(this)
    C[isOutlier] <- naValue
    this <- setSignals(this, C)
  }

  this
}) # dropSegmentationOutliers()



setMethodS3("segmentByCBS", "PairedPSCNData", function(CT, ...) {
  pkg <- "PSCBS"
  require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)

  # To please R CMD check
  data <- as.data.frame(CT)
  CT <- 2* data$CT / data$CN
  segmentByCBS(y=CT, chromosome=data$chromosome, x=data$x, ...)
}) # segmentByCBS()



setMethodS3("segmentByPairedPSCBS", "PairedPSCNData", function(CT, ...) {
  pkg <- "PSCBS"
  require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)

  # To please R CMD check
  data <- as.data.frame(CT)
  CT <- 2* data$CT / data$CN
  segmentByPairedPSCBS(CT=CT, betaT=data$betaT, betaN=data$betaN,
                   muN=data$muN, chromosome=data$chromosome, x=data$x, ...)
}) # segmentByPairedPSCBS()