## ----cleaning, fig.show='hold',warning=FALSE,message=FALSE-------------------- library(basecallQC) fileLocations <- system.file("extdata",package="basecallQC") config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) fileLocations <- system.file(file.path("extdata","testSampleSheets"),package="basecallQC") runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE) read.delim(sampleSheet[1],sep=",",header = TRUE,comment.char = "[") ## ----cleaning2, fig.show='hold',warning=FALSE,message=FALSE------------------- bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE) cleanedSampleSheet <- validateBCLSheet(sampleSheet[1],param=bcl2fastqparams) head(cleanedSampleSheet) ## ----updating, fig.show='hold',warning=FALSE,message=FALSE-------------------- library(basecallQC) fileLocations <- system.file("extdata",package="basecallQC") config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) fileLocations <- system.file(file.path("extdata","testSampleSheets"),package="basecallQC") runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE) read.delim(sampleSheet[2],sep=",",header = TRUE,comment.char = "[") ## ----updating2, fig.show='hold',warning=FALSE,message=FALSE------------------- bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE) cleanedSampleSheet <- validateBCLSheet(sampleSheet[2],param=bcl2fastqparams) head(cleanedSampleSheet) ## ----basemasks, fig.show='hold',warning=FALSE,message=FALSE------------------- fileLocations <- system.file("extdata",package="basecallQC") runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE) bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE) cleanedSampleSheet <- validateBCLSheet(sampleSheet,param=bcl2fastqparams) baseMasks <- createBasemasks(cleanedSampleSheet,param=bcl2fastqparams) baseMasks$index1Mask ## ----submitCommand, fig.show='hold',warning=FALSE,message=FALSE--------------- toSubmit <- createBCLcommand(bcl2fastqparams,cleanedSampleSheet,baseMasks) toSubmit ## ----basecallQCforMetrics, fig.show='hold',eval=T,echo=F,warning=FALSE,message=FALSE---- fileLocations <- system.file("extdata",package="basecallQC") runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE) outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/") bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE) bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet) ## ----bclSummary, fig.show='hold',warning=FALSE,message=FALSE------------------ bclMetrics <- baseCallMetrics(bcl2fastqparams) head(bclMetrics[[1]]) ## ----demuxSummary, fig.show='hold',warning=FALSE,message=FALSE---------------- demuxMetrics <- demultiplexMetrics(bcl2fastqparams) head(demuxMetrics[[1]]) ## ----basecallQC, fig.show='hold',eval=F,warning=FALSE,message=FALSE----------- # fileLocations <- system.file("extdata",package="basecallQC") # runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) # config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) # sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE) # outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/") # bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE) # bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet) # class(bclQC) ## ----basecallQC2, fig.show='hold',eval=F,eval=T,echo=F,warning=FALSE,message=FALSE---- class(bclQC) ## ----tables, fig.show='hold',warning=FALSE,message=FALSE---------------------- summaryConvStatsTable(bclQC,output = "html") summaryDemuxTable(bclQC,output = "html") ## ----plots1, fig.show='hold',warning=FALSE,message=FALSE, fig.width=5, fig.height=5---- passFilterBar(bclQC,groupBy="Sample",metricToPlot = "Yield") ## ----plots2, fig.show='hold',warning=FALSE,message=FALSE, fig.width=5, fig.height=5---- passFilterTilePlot(bclQC,metricToPlot = "Yield") ## ----plots3, fig.show='hold',warning=FALSE,message=FALSE, fig.width=5, fig.height=5---- demuxBarplot(bclQC,groupBy="Sample") ## ----plots4, eval=F, warning=FALSE,message=FALSE------------------------------ # reportBCL(bclQC) ## ----sessionInfo,echo=F,fig.height=30,fig.width=15---------------------------- sessionInfo()