passFilterBar: Barplot of Illumina basecalling statistics for reads passing...

Description Usage Arguments Value Author(s) Examples

Description

Produces a barplot of Illumina basecalling statistics for reads passing filter.

Usage

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

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

## S4 method for signature 'list'
passFilterBar(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

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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 <- passFilterBar(bclQC)

ThomasCarroll/basecallQC documentation built on May 10, 2017, 4:50 p.m.