BCL2FastQparams: The Parameters for BCL2FastQparams object.

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

Description

Parameter class and accessors for use with basecallQC

Parameter class and accessors

Usage

BCL2FastQparams(runXML = NULL, config = NULL, runDir = NULL,
  outDir = NULL, verbose = TRUE)

Arguments

runXML	file path to runParameters.xml ,if not specified looks in top level of run directory.
config	file path to config.ini ,if not specified looks in top level of run directory.
runDir	file path to run directory.
outDir	file path to out directory.
verbose	TRUE or FALSE. Messages on or off. Warnings/errors persist

Details

The BCL2FastQparams object contains slots RunDir, OutDir and RunParameters

• "RunDir" Character string specifying the top level Run directory

• "OutDir" Character string specifying the output directory

• "RunParameters" A data.frame containing the information from runParameters.xml (See vignette for more details).

Value

A BCL2FastQparams object (See details).

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)
BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

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