createBasemasks {basecallQC} | R Documentation

## Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7).

### Description

Parses the Illumina sample sheet for versions >= 2.1.7 and creates basemasks.

### Usage

    createBasemasks(cleanedSampleSheet, param)

### Arguments

`cleanedSampleSheet` | Data.frame of cleaned samplesheet for Illumina basecalling using bcl2Fastq versions >= 2.1.7 (see vignette for more details)
`param` | A BCL2FastQparams object

### Value

A data.frame containing basecall masks per lane for reads and indexes as well as per lane complete basemasks.

### Author(s)

Thomas Carroll and Marian Dore

### 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)
    bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

    cleanedSampleSheet <- validateBCLSheet(sampleSheet,param=bcl2fastqparams)
    basemasks <- createBasemasks(cleanedSampleSheet,param=bcl2fastqparams)

[Package basecallQC version 1.12.0 Index]