validateBCLSheet: Illumina sample sheet cleaning and updating for bcl2Fastq...

Description Usage Arguments Value Author(s) Examples

View source: R/processIlluminaSamplesheets_Functions.R

Description

Parses an Illumina bcl2Fastq sample sheet to create a standardised/updated sample sheet for bcl2Fastq >= Version 2.1.7

Usage

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validateBCLSheet(sampleSheet, param = bcl2fastqparams)

Arguments

sampleSheet

File location of a sample sheet for Illumina basecalling using bcl2Fastq (See vignette for more details).

param

A BCL2FastQparams object

Value

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

Author(s)

Thomas Carroll and Marian Dore

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)
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
cleanedSampleSheet <- validateBCLSheet(sampleSheet,param=bcl2fastqparams)

ThomasCarroll/basecallQC documentation built on May 10, 2017, 4:50 p.m.