Mercurial > repos > shians > shrnaseq
comparison hairpinTool.R @ 9:f1076bfb0ed1
- Fixed tool to actually make use of barcode location options
- Stored variables now properly used in processHairpinReads function
| author | shian_su <registertonysu@gmail.com> |
|---|---|
| date | Wed, 30 Jul 2014 15:13:45 +1000 |
| parents | 548802b3492f |
| children | 8923d4ea858b |
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| 8:548802b3492f | 9:f1076bfb0ed1 |
|---|---|
| 33 # wise test | 33 # wise test |
| 34 # 18.selectOpt -String specifying type of selection for barcode | 34 # 18.selectOpt -String specifying type of selection for barcode |
| 35 # plots | 35 # plots |
| 36 # 19.selectVals -String specifying members selected for barcode | 36 # 19.selectVals -String specifying members selected for barcode |
| 37 # plots | 37 # plots |
| 38 # ### | |
| 38 # | 39 # |
| 39 # OUT: Bar Plot of Counts Per Index | 40 # OUT: Bar Plot of Counts Per Index |
| 40 # Bar Plot of Counts Per Hairpin | 41 # Bar Plot of Counts Per Hairpin |
| 41 # MDS Plot | 42 # MDS Plot |
| 42 # Smear Plot | 43 # Smear Plot |
| 55 library(statmod, quietly=TRUE, warn.conflicts=FALSE) | 56 library(statmod, quietly=TRUE, warn.conflicts=FALSE) |
| 56 library(splines, quietly=TRUE, warn.conflicts=FALSE) | 57 library(splines, quietly=TRUE, warn.conflicts=FALSE) |
| 57 library(edgeR, quietly=TRUE, warn.conflicts=FALSE) | 58 library(edgeR, quietly=TRUE, warn.conflicts=FALSE) |
| 58 library(limma, quietly=TRUE, warn.conflicts=FALSE) | 59 library(limma, quietly=TRUE, warn.conflicts=FALSE) |
| 59 | 60 |
| 60 if (packageVersion("edgeR") < "3.5.23") { | 61 if (packageVersion("edgeR") < "3.5.27") { |
| 61 stop("Please update 'edgeR' to version >= 3.5.23 to run this tool") | 62 stop("Please update 'edgeR' to version >= 3.5.23 to run this tool") |
| 62 } | 63 } |
| 63 | 64 |
| 64 if (packageVersion("limma")<"3.19.19") { | 65 if (packageVersion("limma")<"3.19.19") { |
| 65 message("Update 'limma' to version >= 3.19.19 to see updated barcode graphs") | 66 message("Update 'limma' to version >= 3.19.19 to see updated barcode graphs") |
| 357 | 358 |
| 358 if (inputType=="fastq") { | 359 if (inputType=="fastq") { |
| 359 # Use EdgeR hairpin process and capture outputs | 360 # Use EdgeR hairpin process and capture outputs |
| 360 hpReadout <- capture.output( | 361 hpReadout <- capture.output( |
| 361 data <- processHairpinReads(fastqPath, samplePath, annoPath, | 362 data <- processHairpinReads(fastqPath, samplePath, annoPath, |
| 363 barcodeStart=barStart, barcodeEnd=barEnd, | |
| 362 hairpinStart=hpStart, hairpinEnd=hpEnd, | 364 hairpinStart=hpStart, hairpinEnd=hpEnd, |
| 363 verbose=TRUE) | 365 verbose=TRUE) |
| 364 ) | 366 ) |
| 365 | 367 |
| 366 # Remove function output entries that show processing data or is empty | 368 # Remove function output entries that show processing data or is empty |
| 466 pdf(mdsPdf) | 468 pdf(mdsPdf) |
| 467 plotMDS(data, labels=data$samples$group, col=as.numeric(data$samples$group), | 469 plotMDS(data, labels=data$samples$group, col=as.numeric(data$samples$group), |
| 468 main="MDS Plot") | 470 main="MDS Plot") |
| 469 newEntry <- c("MDS Plot (.pdf)", "mds.pdf") | 471 newEntry <- c("MDS Plot (.pdf)", "mds.pdf") |
| 470 linkData <- rbind(linkData, newEntry) | 472 linkData <- rbind(linkData, newEntry) |
| 473 invisible(dev.off()) | |
| 474 | |
| 475 # BCV Plot | |
| 476 png(bcvPng, width=600, height=600) | |
| 477 plotBCV(data, main="BCV Plot") | |
| 478 imageData <- rbind(imageData, c("BCV Plot", "bcv.png")) | |
| 479 invisible(dev.off()) | |
| 480 | |
| 481 pdf(bcvPdf) | |
| 482 plotBCV(data, main="BCV Plot") | |
| 483 newEntry <- c("BCV Plot (.pdf)", "bcv.pdf") | |
| 471 invisible(dev.off()) | 484 invisible(dev.off()) |
| 472 | 485 |
| 473 if (workMode=="classic") { | 486 if (workMode=="classic") { |
| 474 # Assess differential representation using classic exact testing methodology | 487 # Assess differential representation using classic exact testing methodology |
| 475 # in edgeR | 488 # in edgeR |