baseCallMetrics {basecallQC} | R Documentation |
Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).
baseCallMetrics(bcl2fastqparams)
bcl2fastqparams |
A BCL2FastQparams object as created by BCL2FastQparams() constructor. |
A list of length two containing the full basecalling metrics from a Run (using Run's ConversionStats.xml file). Contains an unsummarised data.frame and basecalling metrics summarised to Sample, Lane, Sample by lane, and Sample by Lane and Tile.
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) convMetrics <- baseCallMetrics(bcl2fastqparams)