R/AbstractCBS.clearCalls.R

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

# Removes all segment calls and corresponding parameter estimates.
setMethodS3("clearCalls", "AbstractCBS", function(fit, ...) {
  segs <- fit$output
  params <- fit$params

  # Drop all calls
  excl <- grep("Call$", colnames(segs))
  if (length(excl) > 0L) {
    segs <- segs[,-excl]
  }

  # Drop all call parameters (AD HOC!)
  for (ff in c("deltaROH", "deltaAB", "deltaLOH")) {
    params[[ff]] <- NULL
  }

  fit$output <- segs
  fit$params <- params

  invisible(fit)
}, protected=TRUE)



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# HISTORY
# 2013-10-24
# o Added clearCalls() for AbstractCBS.
# o Created.
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