passFilterBoxplot {basecallQC} | R Documentation

## Boxplot of Illumina basecalling statistics for reads passing filter.

### Description

Produces a boxplot of basecalling statistics for reads passing filter.

### Usage

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

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

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

### Arguments

`object` | A basecallQC object or list from call to baseCallMetrics()
`groupBy` | Character vector of how data is grouped for plotting. Should be either "Project","Sample","Lane","Tile","ReadNumber".
`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 <- passFilterBoxplot(bclQC,groupBy = "Sample")

[Package basecallQC version 1.6.0 Index]