makeFQTable: Generate an HTML table linking to per sample summary fastq QC...

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

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")

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