BCL2FastQparams-class {basecallQC} | R Documentation

## The Parameters for BCL2FastQparams object.

### 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)

[Package basecallQC version 1.4.0 Index]