passFilterBoxplot: Boxplot of Illumina basecalling statistics for reads passing...

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

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")

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