reportBCL {basecallQC} | R Documentation

## Generate basecallQC report

### 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")

[Package basecallQC version 1.4.0 Index]