inst/rsp-ex/TCGA,OV,testSet,pairs,fracB,v3/R/extractListOfCopyNumbers.list.R

In HenrikBengtsson/aroma.cn.eval: Objective Assessment of Copy-Number Estimates

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setMethodS3("extractListOfCopyNumbers", "list", function(this, name, chromosome, region=NULL, targetChipType=NULL, truth=NULL, what=c("log2ratios", "ratios"), ..., force=TRUE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'name':
  if (is.list(name)) {
    chromosome <- name$chromosome;
    region <- name$region;
    name <- name$name;
  }
 
  # Argument 'targetChipType':
  if (!is.null(targetChipType)) {
    targetChipType <- Arguments$getCharacter(targetChipType);
  }

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


  verbose && enter(verbose, "extractListOfCopyNumbers()");


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Extract CNs
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Extract list of files
  dfList <- lapply(this, FUN=function(ds) {
    idx <- indexOf(ds, name);
    getFile(ds, idx);
  });

  cnList <- list();
  for (kk in seq(dfList)) {
    df <- dfList[[kk]];

    # Extract only units that exist in target chip type?
    units <- NULL;
    if (!is.null(targetChipType)) {
      verbose && enter(verbose, "Identifying target units");
      chipType <- getChipType(df);
      if (chipType != targetChipType) {
        units <- matchUnitsToTargetCdf(chipType, targetChipType);
      }
      verbose && str(verbose, units);
      verbose && exit(verbose);
    }

    # Extract copy numbers
    verbose && enter(verbose, "Extracting CNs");
    cn <- extractRawCopyNumbers(df, chromosome=chromosome, 
                                            region=region, units=units);
    verbose && print(verbose, cn);
    verbose && exit(verbose);

    # Add true CN functions?
    if (!is.null(truth)) {
##      cn <- SegmentedCopyNumbers(cn, states=truth);
      cn$state <- truth;
    }

    cnList[[kk]] <- cn;
  } # for (kk ...)
  names(cnList) <- names(dfList);

  # Sanity check
  if (!is.null(targetChipType)) {
    nbrOfUnits <- sapply(cnList, FUN=nbrOfLoci);
    stopifnot(length(unique(nbrOfUnits)) == 1);
  }

  verbose && exit(verbose);

  cnList;
});

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# HISTORY:
# 2009-02-23
# o Created.
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