Description Usage Arguments Value Author(s) Examples
Parses the Illumina sample sheet for versions >= 2.1.7 and creates basemasks.
1 | createBasemasks(cleanedSampleSheet, param)
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cleanedSampleSheet |
Data.frame of cleaned samplesheet for Illumina basecalling using bcl2Fastq versions >= 2.1.7 (see vignette for more details) |
param |
A BCL2FastQparams object |
A data.frame containing basecall masks per lane for reads and indexes as well as per lane complete basemasks.
Thomas Carroll and Marian Dore
1 2 3 4 5 6 7 8 | 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)
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