basecallQC-class {basecallQC} | R Documentation

## The basecallQC object and constructor.

### 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)

[Package basecallQC version 1.12.0 Index]