passFilterTilePlot {basecallQC} | R Documentation |
Produces a plot of metric per Tile for basecalling statistics of reads passing/failing filter.
## S4 method for signature 'baseCallQC' passFilterTilePlot(object,metricToPlot) ## S4 method for signature 'basecallQC' passFilterTilePlot(object = "basecallQC", metricToPlot = "Yield") ## S4 method for signature 'list' passFilterTilePlot(object = "basecallQC", metricToPlot = "Yield")
object |
A basecallQC object or list from call to baseCallMetrics() |
metricToPlot |
Character vector defining which metric will be displayed in plot. Should be either "Yield","Yield30","QualityScoreSum" or "ClusterCount". |
A ggplot2 object.
Thomas Carroll and Marian Dore
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) plot <- passFilterTilePlot(bclQC,metricToPlot="Yield")