makeFQTable {basecallQC} | R Documentation

## Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead

### Description

Creates an HTML table linking to per sample summary fastq QC statistics from ShortRead

### Usage

    makeFQTable(object, output = "static")

### Arguments

`object` | A basecall QC object as returned from basecallQC function
`output` | Whether the report contains frozen or sortable tables. Options are "static" and "html"

### Value

A HTML table for reporting fastq QC results from ShortRead. Table contains read counts and links to ShortRead QA reports per sample.

### 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)
    #makeFQTable(bclQC,output="static")

[Package basecallQC version 1.4.0 Index]