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comparison QDNAseq.R @ 29:4c4e4d88779c draft

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Uploaded
author stef
date Wed, 18 Jun 2014 05:33:04 -0400
parents 40ae95ad9d8c
children 647143d0c884
comparison
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28:40ae95ad9d8c 29:4c4e4d88779c
282 copyNumbersSmooth <- smoothOutlierBins( copyNumbersNormalized ) 282 copyNumbersSmooth <- smoothOutlierBins( copyNumbersNormalized )
283 sampleNames <- readCountsFiltered@phenoData@data$name 283 sampleNames <- readCountsFiltered@phenoData@data$name
284 284
285 ## save objects to output dir 285 ## save objects to output dir
286 saveRDS( readCounts, robjReadCoPath ); 286 saveRDS( readCounts, robjReadCoPath );
287 saveRDS( copyNumbersSmooth, robjCopyNrPath );s 287 saveRDS( copyNumbersSmooth, robjCopyNrPath );
288 exportBins(copyNumbersSmooth, file=igvCopyNrName, format="igv") 288 exportBins(copyNumbersSmooth, file=igvCopyNrName, format="igv")
289 289
290 ## also save objects for galaxy history output if requested 290 ## also save objects for galaxy history output if requested
291 if ( doOutputReadcountsRds ){ 291 if ( doOutputReadcountsRds ){
292 saveRDS( readCountsFiltered, readCountsDatasetFile ); 292 saveRDS( readCountsFiltered, readCountsDatasetFile );