reportBCL: Generate basecallQC report

Description Usage Arguments Value Author(s) Examples

Description

Creates a summary report from basecalling and demultiplexing metrics.

Usage

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## 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

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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)
bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
reportBCL(bclQC,"TestReport.html",output="html")

ThomasCarroll/basecallQC documentation built on May 10, 2017, 4:50 p.m.