baseCallMetrics {basecallQC} | R Documentation

## Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).

### Description

Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).

### Usage

    baseCallMetrics(bcl2fastqparams)

### Arguments

`bcl2fastqparams` | A BCL2FastQparams object as created by BCL2FastQparams() constructor.

### Value

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.

### 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)
    convMetrics <- baseCallMetrics(bcl2fastqparams)

[Package basecallQC version 1.10.0 Index]