baseCallMetrics: Gather basecalling metrics from a Run (using Run's...

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

Description

Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).

Usage

baseCallMetrics(bcl2fastqparams)

Arguments

bcl2fastqparams

A BCL2FastQparams object as created by BCL2FastQparams() constructor.

Value

A list of length two containing the full basecalling metrics from a Run (using Run's ConversionStats.xml file). Contains an unsummarised data.frame and basecalling metrics summarised to Sample, Lane, Sample by lane, and Sample by Lane and Tile.

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)
convMetrics <- baseCallMetrics(bcl2fastqparams)

basecallQC documentation built on Nov. 8, 2020, 8:03 p.m.