| Previous changeset 8:548802b3492f (2014-05-02) Next changeset 10:8923d4ea858b (2014-08-12) |
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Commit message:
- Fixed tool to actually make use of barcode location options - Stored variables now properly used in processHairpinReads function |
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modified:
hairpinTool.R hairpinTool.xml |
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| diff -r 548802b3492f -r f1076bfb0ed1 hairpinTool.R --- a/hairpinTool.R Fri May 02 17:22:24 2014 +1000 +++ b/hairpinTool.R Wed Jul 30 15:13:45 2014 +1000 |
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| @@ -35,6 +35,7 @@ # plots # 19.selectVals -String specifying members selected for barcode # plots +# ### # # OUT: Bar Plot of Counts Per Index # Bar Plot of Counts Per Hairpin @@ -57,7 +58,7 @@ library(edgeR, quietly=TRUE, warn.conflicts=FALSE) library(limma, quietly=TRUE, warn.conflicts=FALSE) -if (packageVersion("edgeR") < "3.5.23") { +if (packageVersion("edgeR") < "3.5.27") { stop("Please update 'edgeR' to version >= 3.5.23 to run this tool") } @@ -359,6 +360,7 @@ # Use EdgeR hairpin process and capture outputs hpReadout <- capture.output( data <- processHairpinReads(fastqPath, samplePath, annoPath, + barcodeStart=barStart, barcodeEnd=barEnd, hairpinStart=hpStart, hairpinEnd=hpEnd, verbose=TRUE) ) @@ -470,6 +472,17 @@ linkData <- rbind(linkData, newEntry) invisible(dev.off()) +# BCV Plot +png(bcvPng, width=600, height=600) +plotBCV(data, main="BCV Plot") +imageData <- rbind(imageData, c("BCV Plot", "bcv.png")) +invisible(dev.off()) + +pdf(bcvPdf) +plotBCV(data, main="BCV Plot") +newEntry <- c("BCV Plot (.pdf)", "bcv.pdf") +invisible(dev.off()) + if (workMode=="classic") { # Assess differential representation using classic exact testing methodology # in edgeR |
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| diff -r 548802b3492f -r f1076bfb0ed1 hairpinTool.xml --- a/hairpinTool.xml Fri May 02 17:22:24 2014 +1000 +++ b/hairpinTool.xml Wed Jul 30 15:13:45 2014 +1000 |
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| @@ -1,11 +1,12 @@ -<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.9"> +<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.11"> <description> Analyse hairpin differential representation using edgeR </description> <requirements> - <requirement type="R-module" version="3.5.27">edgeR</requirement> - <requirement type="R-module" version="3.18.13">limma</requirement> + <requirement type="R-module" version="3.6.2">edgeR</requirement> + <requirement type="R-module" version="3.20.7">limma</requirement> + <requirement type="package" version="3.0.3">R_3_0_3</requirement> </requirements> <stdio> |