basecallQC: The basecallQC object and constructor.

Description Usage Arguments Details Value Examples

Description

Object and method to handle Illumina basecalling/demultiplexing inputs and output files. Provides sample sheet cleanup, basecall command and summary QC statistics for basecalling/demultiplexing.

The basecallQC object and constructor.

Usage

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basecallQC(bcl2fastqparams, RunMetaData = NULL, sampleSheet = NULL,
  doFQMetric = FALSE)

Arguments

bcl2fastqparams

A BCL2FastQparams object as created by BCL2FastQparams() constructor.

RunMetaData

Any run metadata to attach (data.frame)

sampleSheet

A sample sheet for Illumina basecalling using bcl2Fastq (See vignette for more details).

doFQMetric

TRUE or FALSE. Perform ShortRead FastQ quality assessment using ShortRead's qa and report function

Details

The basecallQC object contains slots BCL2FastQparams, cleanedSampleSheet, baseMasks, BCLCommand, baseCallMetrics, demultiplexMetrics and fqQCmetrics.

Value

basecallQC a basecallQC object (See details for more information)

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)

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