R/PairedPSCBS.unTumorBoost.R

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

# @title "Re-calculates the segmented profile using non-TumorBoost BAFs"
setMethodS3("unTumorBoost", "PairedPSCBS", function(fit, ..., verbose=FALSE) {
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enterf(verbose, "Relcalculating %s profile without TumorBoost", class(fit)[1L])

  # Nothing to do?
  if (!fit$params$tbn) {
    verbose && cat(verbose, "Profile is not from TumorBoost signals. Skipping.")
    verbose && exit(verbose)
    return(fit)
  }

  verbose && enter(verbose, "Updating locus-level data")
  data <- getLocusData(fit)
  data$betaTN <- data$betaT
  isHet <- !is.na(data$rho)
  data$rho[isHet] <- 2*abs(data$betaTN[isHet]-1/2)
  fit$data <- data
  verbose && exit(verbose)

  verbose && enter(verbose, "Updating segments")
  segs <- getSegments(fit)
  segs$abCall <- NULL
  segs$lohCall <- NULL
  fit$output <- segs
  verbose && exit(verbose)

  verbose && enter(verbose, "Updating parameters")
  params <- fit$params
  params$tbn <- FALSE
  params$deltaAB <- params$alphaAB <- NULL
  params$deltaLowC1 <- params$alphaLowC1 <- NULL
  fit$params <- params
  verbose && exit(verbose)

  verbose && enter(verbose, "Resetting miscellaneous parameters and estimates")
  fit$changepoints <- NULL
  fit$deshearC1C2 <- NULL
  fit$cScaled <- NULL
  fit$kappa <- NULL
  fit$scale <- NULL
  fit <- clearBootstrapSummaries(fit, verbose=less(verbose, 50))
  verbose && exit(verbose)

  verbose && enter(verbose, "Update segment levels")
  fit <- updateMeans(fit, verbose=less(verbose, 50))
  verbose && exit(verbose)

  verbose && exit(verbose)

  fit
}, protected=TRUE) # unTumorBoost()


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# HISTORY
# 2014-03-28
# o Added unTumorBoost() for PairedPSCBS.
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