basecallQC: The basecallQC object and constructor.

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

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

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.

• "BCL2FastQparams" A BCL2FastQparams object

• "cleanedSampleSheet" A data.frame containing the cleaned sample sheet for Illumina basecalling using bcl2Fastq versions >= 2.1.7

• "baseMasks" A data.frame containing basecall masks per lane for use with bcl2Fastq versions >= 2.1.7. Basemasks in data.frame for reads and indexes as well as the total basemasks for each lane.

• "BCLCommand" A character string containing the command to be used for basecalling using bcl2Fastq (versions >= 2.1.7).

• "baseCallMetrics" A list containing the full basecalling metrics from ConversionStats.xml. Contains an unsummarised data.frame and basecalling metrics summarised to Sample, Lane, Sample by lane, and Sample by Lane and Tile

• "demultiplexMetrics" A list containing the full demultiplexing metrics from DemultiplexingStats.xml. Contains an unsummarised data.frame and demultiplexing metrics filtered to per Sample metrics

• "fqQCmetrics" A list containing a data.frame of read counts and links to ShortRead QA reports and a ShortRead QA object containing quality information for generated fastQs.

Value

basecallQC a basecallQC object (See details for more information)

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)

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