Mercurial > repos > shians > shrnaseq

comparison hairpinTool.R @ 11:c0a76e30d61b

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- Removed max on cpm filtering. Really shouldn't have been there in the first place. - Added explicit arguments to processHairpinReads in R.
author shian_su <registertonysu@gmail.com>
date Tue, 30 Sep 2014 16:36:12 +1000
parents 8923d4ea858b
children ebb4cb1e8e35
comparison
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10:8923d4ea858b 11:c0a76e30d61b
357 } 357 }
358 358
359 if (inputType=="fastq") { 359 if (inputType=="fastq") {
360 # Use EdgeR hairpin process and capture outputs 360 # Use EdgeR hairpin process and capture outputs
361 hpReadout <- capture.output( 361 hpReadout <- capture.output(
362 data <- processHairpinReads(fastqPath, samplePath, annoPath, 362 data <- processHairpinReads(readfile=fastqPath,
363 barcodefile=samplePath,
364 hairpinfile=annoPath,
363 barcodeStart=barStart, barcodeEnd=barEnd, 365 barcodeStart=barStart, barcodeEnd=barEnd,
364 hairpinStart=hpStart, hairpinEnd=hpEnd, 366 hairpinStart=hpStart, hairpinEnd=hpEnd,
365 verbose=TRUE) 367 verbose=TRUE)
366 ) 368 )
367 369