reportBCL: Generate basecallQC report

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

Description

Creates a summary report from basecalling and demultiplexing metrics.

Usage

## S4 method for signature 'basecallQC'
reportBCL(object,reportOut,reportOutDir,output,reportRMDfile,FQQC)

## S4 method for signature 'basecallQC'
reportBCL(object = "basecallQC",
  reportOut = "report.html", reportOutDir = getwd(), output = "static",
  reportRMDfile = NULL, FQQC = FALSE)

Arguments

object	A basecall QC object as returned from basecallQC() function
reportOut	Name of report file
reportOutDir	Directory for the report file
output	Whether the report contains frozen or sortable tables. Options are "static" and "html"
reportRMDfile	RMD to be used for reporting. (Default uses standard report template)
FQQC	TRUE or FALSE, whether to run ShortRead fastq QC on any fastQ in output directory.

Value

An HTML report is written to file.

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)
reportBCL(bclQC,"TestReport.html",output="html")

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