inst/testScripts/publications/CalMaTe/Z03.plots,byUnits.R

In calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

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# Title:
# Author: Henrik Bengtsson
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# Loading support files
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# Find the pathname and directory of this script
library("R.utils");
pathname <- names(findSourceTraceback())[1];
path <- dirname(pathname);

# Loading include files
pathT <- file.path(path, "R/");
sourceDirectory(path=pathT);


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# Calibrated or not?
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calTag <- textMenu(calTags, title="Choose calibration method:", value=TRUE);
if (calTag == "<none>") calTag <- NULL;


dsList <- loadSets(dataSet, tags=c(tags, calTag), chipType=chipType, verbose=verbose);
verbose && print(verbose, dsList);

# Sanity check
# stopifnot(all(sapply(dsList, FUN=length) == 40));


# Translated data set tags
dsTags <- tags(fullname(dataSet, getTags(dsList[[1]])));
dsTags <- gsub("ACC,-XY,BPN,-XY,RMA,FLN,-XY", "ASCRMAv2", dsTags);
dsTags <- gsub("ACC,-XY,BPN,-XY,AVG,FLN,-XY", "ASCRMAv2", dsTags);
dsTags <- gsub("CMTN", "CalMaTe", dsTags);
dsTags <- dropTags(dsTags, drop="refs=N");


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# Extracting signals
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units <- 1000+1:100;
dd <- extractCACB(dsList, units=units);

tagsT <- dsTags;
for (uu in seq_along(units)) {
  unit <- units[uu];
  unitTag <- sprintf("unit%06d", unit);
  unitName <- unit;

  ddT <- dd[uu,,];

  tags <- c(tagsT, unitTag, "CACB");
  toPNG(name=sampleName, tags=tags, width=840, {
    plotMultiArrayCACB(ddT, unitName=unitName, tagsT=tagsT);
  });
} # for (uu ...)


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# HISTORY:
# 2011-03-10 [HB]
# o Created.
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