passFilterTileplot: Tile plot of Illumina basecalling statistics for reads...

In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

Description

Produces a plot of metric per Tile for basecalling statistics of reads passing/failing filter.

Usage

## 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")

Arguments

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".

Value

A ggplot2 object.

Author(s)

Thomas Carroll and Marian Dore

Examples

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")

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.