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AromaUnitFracBCnBinarySet.exportFracBDiffSet.R
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AromaUnitFracBCnBinarySet.exportFracBDiffSet.R
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setMethodS3("exportFracBDiffSet", "AromaUnitFracBCnBinarySet", function(this, ref, ..., tags=NULL, overwrite=FALSE, rootPath="rawCnData", verbose=FALSE) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
nbrOfFiles <- length(this)
if (nbrOfFiles == 0L) {
throw("Nothing to export. ", class(this)[1], " is empty: ", getFullName(this))
}
nbrOfUnits <- nbrOfUnits(getOneFile(this))
chipType <- getChipType(this)
# Argument 'ref':
if (inherits(ref, "AromaUnitFracBCnBinaryFile")) {
refList <- rep(list(ref), nbrOfFiles)
refSet <- AromaUnitFracBCnBinarySet(refList)
# Not needed anymore
refList <- NULL
}
if (inherits(ref, "AromaUnitFracBCnBinarySet")) {
if (getChipType(ref) != chipType) {
throw("Chip type of argument 'ref' does not match the data set: ", getChipType(ref), " != ", chipType)
}
df <- getOneFile(ref)
if (nbrOfUnits(df) != nbrOfUnits) {
throw("Number of units in argument 'ref' does not match the data set: ", nbrOfUnits(ref), " != ", nbrOfUnits)
}
refSet <- ref
} else {
throw("Argument 'ref' must be of class AromaUnitFracBCnBinary{File|Set}: ", class(ref)[1])
}
# Argument 'tags':
tags <- Arguments$getTags(tags, collapse=",")
# Argument 'verbose':
verbose <- Arguments$getVerbose(verbose)
if (verbose) {
pushState(verbose)
on.exit(popState(verbose))
}
verbose && enter(verbose, "Calculating CN ratios")
dataSet <- getFullName(this)
verbose && cat(verbose, "Data set: ", dataSet)
platform <- getPlatform(this)
verbose && cat(verbose, "Platform: ", platform)
chipType <- getChipType(this)
verbose && cat(verbose, "Chip type: ", chipType)
nbrOfFiles <- length(this)
verbose && cat(verbose, "Number of files: ", nbrOfFiles)
verbose && cat(verbose, "Reference set:")
verbose && print(verbose, refSet)
dataSetOut <- paste(c(dataSet, tags), collapse=",")
verbose && cat(verbose, "Output data set: ", dataSetOut)
chipTypeS <- getChipType(this, fullname=FALSE)
outPath <- file.path(rootPath, dataSetOut, chipTypeS)
outPath <- Arguments$getWritablePath(outPath)
verbose && cat(verbose, "Output path: ", outPath)
ratioTag <- "diff"
typeTags <- paste(c(ratioTag, "fracB"), collapse=",")
for (kk in seq_along(this)) {
df <- this[[kk]]
verbose && enter(verbose, sprintf("File %d ('%s') of %d", kk, getName(df), nbrOfFiles))
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up output filename
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dfR <- refSet[[kk]]
refName <- getFullName(dfR)
refName <- gsub(",(fracB)", "", refName)
refTag <- sprintf("ref=%s", refName)
fullname <- getFullName(df)
fullname <- gsub(",(fracB)", "", fullname)
fullname <- paste(c(fullname, refTag, typeTags), collapse=",")
filename <- sprintf("%s.asb", fullname)
pathname <- file.path(outPath, filename)
verbose && cat(verbose, "Pathname: ", pathname)
if (!overwrite && isFile(pathname)) {
verbose && cat(verbose, "Nothing to do. File already exists.")
verbose && exit(verbose)
next
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allocating
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Allocating (temporary) output file")
pathnameT <- pushTemporaryFile(pathnameT, verbose=verbose)
asb <- AromaUnitSignalBinaryFile$allocate(pathnameT, nbrOfRows=nbrOfUnits(df), platform=platform, chipType=chipType)
verbose && print(verbose, asb)
verbose && exit(verbose)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Calculating relative CNs
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Reading data from total file")
beta <- extractMatrix(df, drop=TRUE, verbose=verbose)
# Sanity check
verbose && str(verbose, beta)
verbose && exit(verbose)
verbose && enter(verbose, "Calculating differences")
betaR <- extractMatrix(dfR, drop=TRUE, verbose=verbose)
verbose && str(verbose, betaR)
# Sanity check
.stop_if_not(length(betaR) == length(beta))
dBeta <- beta - betaR
verbose && str(verbose, dBeta)
# Not needed anymore
beta <- betaR <- NULL
verbose && exit(verbose)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Storing relative CNs
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Updating temporary output file")
# Store data
asb[,1] <- dBeta
# Not needed anymore
dBeta <- NULL
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Updating file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
refFile <- list(
dataSet=dataSet,
fullName=getFullName(dfR),
filename=getFilename(dfR),
checksum=getChecksum(dfR)
)
footer <- readFooter(asb)
footer$srcFiles <- list(
srcFile = list(
dataSet=dataSet,
fullName=getFullName(df),
filename=getFilename(df),
checksum=getChecksum(df)
),
refFile = refFile
)
writeFooter(asb, footer)
# Not needed anymore
footer <- refFile <- NULL
verbose && exit(verbose)
# Renaming temporary file
pathname <- popTemporaryFile(pathnameT, verbose=verbose)
verbose && exit(verbose)
verbose && exit(verbose)
} # for (kk ...)
verbose && enter(verbose, "Setting up output data sets")
pattern <- sprintf("%s[.]asb$", typeTags)
res <- AromaUnitFracBCnBinarySet$byPath(outPath, pattern=pattern)
verbose && exit(verbose)
verbose && exit(verbose)
invisible(res)
}, protected=TRUE) # exportFracBDiffSet()