passFilterTilePlot {basecallQC} | R Documentation

## Tile plot of Illumina basecalling statistics for reads passing filter.

### 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")

[Package basecallQC version 1.12.0 Index]