Mercurial > repos > stef > qdnaseq_test
diff QDNAseq.R @ 27:f89205f51e27 draft default tip
Uploaded
| author | stef |
|---|---|
| date | Mon, 06 Jul 2015 05:41:08 -0400 |
| parents | 4943308e95fc |
| children |
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--- a/QDNAseq.R Mon Jul 06 05:38:44 2015 -0400 +++ b/QDNAseq.R Mon Jul 06 05:41:08 2015 -0400 @@ -290,12 +290,12 @@ ## proceed with segmenting / calling if requested if ( doSegment ){ - copyNumbersSegmented <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD, transformFun="sqrt" ) + copyNumbersSegmented <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD, transformFun=c("sqrt") ) copyNumbersSegmented <- normalizeSegmentedBins( copyNumbersSegmented ) outputData <- copyNumbersSegmented outputType <- 'segments' - igvPath <- paste( outputPath, '/', rdsSegmName, sep='') - rdsPath <- paste( outputPath, '/', igvSegmName, sep='') + igvPath <- paste( outputPath, '/', igvSegmName, sep='') + rdsPath <- paste( outputPath, '/', rdsSegmName, sep='') } if ( doCall ){ copyNumbersCalled <- callBins(copyNumbersSegmented)