baseCallMetrics: Gather basecalling metrics from a Run (using Run's...
In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files
Description
Usage
Arguments
Value
Examples
Description
Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).
Usage
1
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
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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)
outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
convMetrics <- baseCallMetrics(bcl2fastqparams)
ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.
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Description Usage Arguments Value Examples
Description
Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).
Usage
1 | 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
1 2 3 4 5 6 7 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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