summaryConvStatsTable: Creates an HTML table of per sample summary statistics from...

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

Description

Creates an HTML table of per sample summary statistics from basecalling results

Usage

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

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

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

Arguments

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

Value

An HTML table for reporting basecalling 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.