summaryDemuxTable: Generate an HTML table of per sample summary demultiplexing...

In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

Description

Generate an HTML table of per sample summary demultiplexing statistics

Usage

## S4 method for signature 'baseCallQC'
summaryDemuxTable(object)

## S4 method for signature 'basecallQC'
summaryDemuxTable(object = "basecallQC",
  output = "static")

## S4 method for signature 'list'
summaryDemuxTable(object = "basecallQC", output = "static")

Arguments

object	A basecallQC object or list from call to demultiplexMetrics()
output	Whether the report contains frozen or sortable tables. Options are "static" and "html"

Value

An HTML table for reporting demultiplexing results.

Author(s)

Thomas Carroll

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)
bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
summaryDemuxTable(bclQC,output="static")

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.