Mercurial > repos > stef > qdnaseq_test

comparison QDNAseq.R @ 27:f89205f51e27 draft default tip

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Uploaded
author stef
date Mon, 06 Jul 2015 05:41:08 -0400
parents 4943308e95fc
children
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26:069289631381 27:f89205f51e27
288 rdsPath <- paste( outputPath, '/', rdsCopyName, sep='') 288 rdsPath <- paste( outputPath, '/', rdsCopyName, sep='')
289 igvPath <- paste( outputPath, '/', igvCopyName, sep='') 289 igvPath <- paste( outputPath, '/', igvCopyName, sep='')
290 290
291 ## proceed with segmenting / calling if requested 291 ## proceed with segmenting / calling if requested
292 if ( doSegment ){ 292 if ( doSegment ){
293 copyNumbersSegmented <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD, transformFun="sqrt" ) 293 copyNumbersSegmented <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD, transformFun=c("sqrt") )
294 copyNumbersSegmented <- normalizeSegmentedBins( copyNumbersSegmented ) 294 copyNumbersSegmented <- normalizeSegmentedBins( copyNumbersSegmented )
295 outputData <- copyNumbersSegmented 295 outputData <- copyNumbersSegmented
296 outputType <- 'segments' 296 outputType <- 'segments'
297 igvPath <- paste( outputPath, '/', rdsSegmName, sep='') 297 igvPath <- paste( outputPath, '/', igvSegmName, sep='')
298 rdsPath <- paste( outputPath, '/', igvSegmName, sep='') 298 rdsPath <- paste( outputPath, '/', rdsSegmName, sep='')
299 } 299 }
300 if ( doCall ){ 300 if ( doCall ){
301 copyNumbersCalled <- callBins(copyNumbersSegmented) 301 copyNumbersCalled <- callBins(copyNumbersSegmented)
302 outputData <- copyNumbersCalled 302 outputData <- copyNumbersCalled
303 outputType <- 'calls' 303 outputType <- 'calls'