demuxBoxplot {basecallQC} | R Documentation

## Boxplot of Illumina demultiplexing statistics.

### Description

Produces a boxplot of demultiplexing statistics of reads with perfect/mismatched barcode.

### Usage

    ## S4 method for signature 'baseCallQC'
    demuxBoxplot(object,groupBy)

    ## S4 method for signature 'basecallQC'
    demuxBoxplot(object = "basecallQC",
      groupBy = c("Lane"))

    ## S4 method for signature 'list'
    demuxBoxplot(object = "basecallQC", groupBy = c("Lane"))

### Arguments

`object` | A basecallQC object or list from call to demultiplexMetrics()
`groupBy` | Character vector of how data is grouped for plotting. Should be either "Project","Sample" or "Lane".

### 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 <- demuxBoxplot(bclQC)

[Package basecallQC version 1.8.0 Index]