Mercurial > repos > shians > shrnaseq

comparison hairpinTool.R @ 15:5a917ea5bed2

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- Fixed read requirement report statistic.
author shian_su <registertonysu@gmail.com>
date Mon, 12 Jan 2015 16:31:48 +1100
parents 7aaa9bc23e3c
children 525bf4364896
comparison
equal deleted inserted replaced
14:44130e484a97 15:5a917ea5bed2
415 } 415 }
416 } 416 }
417 417
418 if (inputType == "fastq" || inputType == "pairedFastq") { 418 if (inputType == "fastq" || inputType == "pairedFastq") {
419 # Use EdgeR hairpin process and capture outputs 419 # Use EdgeR hairpin process and capture outputs
420
420 hpReadout <- capture.output( 421 hpReadout <- capture.output(
421 data <- processAmplicons(readfile=fastqPath, readfile2=fastqPathRev, 422 data <- processAmplicons(readfile=fastqPath, readfile2=fastqPathRev,
422 barcodefile=samplePath, 423 barcodefile=samplePath,
423 hairpinfile=annoPath, 424 hairpinfile=annoPath,
424 barcodeStart=barStart, barcodeEnd=barEnd, 425 barcodeStart=barStart, barcodeEnd=barEnd,
986 "count-per-million.") 987 "count-per-million.")
987 ListItem(tempStr) 988 ListItem(tempStr)
988 } 989 }
989 990
990 if (sampleReq != 0) { 991 if (sampleReq != 0) {
991 tempStr <- paste("Samples that did not produce more than", sampleReq, 992 tempStr <- paste("Samples that did not produce more than", readReq,
992 "counts were filtered out.") 993 "counts were filtered out.")
993 ListItem(tempStr) 994 ListItem(tempStr)
994 995
995 tempStr <- paste0(sampleFilterCount, " samples were filtered out for low ", 996 tempStr <- paste0(sampleFilterCount, " samples were filtered out for low ",
996 "counts.") 997 "counts.")