## ---- cleaning, fig.show='hold',warning=FALSE,message=FALSE------------------- library(basecallQC) fileLocations <- system。testSampleSheets”），package =“ basecallqc”）runxml < - dir（fileLocations，模式=“ runparameters.xml”，full.names = true）samplesheet sampleshEet <-dir（fileLocations，fileLocations，pattern ='*\\ \ \。。names = true）read.delim（SampleSheet [1]，sep =“，”，header = true，comment.char =“ [“）## ----清洁2，fig.show ='hold'，hold'，警告= false,message=FALSE------------------ bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE) cleanedSampleSheet <- validateBCLSheet(sampleSheet[1]，param = bcl2fastqparams）head（cleanedsamplesheet）## ----更新，fig.show ='hold ='hold'，harning'，harning = false，message = false --------------------------------------------------------------------------------------------------------------------------------------------library（basecallqc）fileLocations <-system.file（“ extdata”，package =“ basecallqc”）config < - dir（fileLocations，tatter =“ 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，tatter =“*\\。csv”，full.names = true）"[") ## ---- updating2, fig.show='hold',warning=FALSE,message=FALSE------------------ bcl2fastqparams <- BCL2FastQparams(runxml，config，rundir = getwd（），verbose = false）calledsamplesheet <-ValidateBClsheet（SampleSheet [2]，param = bcl2fastqparams）head（cleanedsamplesheet）## ----------------------------------------------------------false，messages = false -------------------- fileLocations <-System.file（“ extdata”，package =“ basecallqc”）runxml < - dir（fileLocations，tatter otates =''runParameters.xml“，full.names = true）config < - dir（fileLocations，tatter =“ config.ini”，full.names = true）samplesheet <-dir（fileLocations，fileLocations，pattern =“*\\。csv”，full full full.names = true）bcl2fastqparams <-bcl2fastqparams（runxml，config，rundir = getwd（），详细信息= false）清洁sa​​mpleshEet <-validateBclsheet（samplesheet，param = bcl2fastqparams）basemasks <-createBasemasks（cleanedSampleshEet，param = bcl2fastqparams）basemasks $ index1mask ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sistscommand，firf.show.show =''''，warowning''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()