writeTargetsRef {systemPipeR} | R Documentation

## Generate targets file with reference

### Description

Generates targets file with sample-wise reference as required for some NGS applications, such as ChIP-Seq containing input samples. The reference sample information needs to be provided in the input file in a column called `SampleReference` where the values reference the labels used in the `SampleName` column. Sample rows without reference assignments will be removed automatically.

### Usage

    writeTargetsRef(infile, outfile, silent = FALSE, overwrite = FALSE, ...)

### Arguments

`infile` | Path to input targets file.
`outfile` | Path to output targets file.
`silent` | If set to `TRUE`, all messages returned by the function will be suppressed.
`overwrite` | If set to `TRUE`, existing files of same name will be overwritten.
`...` | To pass on additional arguments.

### Value

Generates modified targets file with the paths to the reference samples in the second column named `FileName2`. Note, sample rows not assigned reference samples are removed automatically.

### Author(s)

Thomas Girke

### See Also

`writeTargetsout`, `mergeBamByFactor`

### Examples

    ## Path to input targets file
    targets <- system.file("extdata", "targets_chip.txt", package="systemPipeR")

    ## Not run:
    ## Write modified targets file with reference (e.g. input) sample
    writeTargetsRef(infile=targets, outfile="~/targets_refsample.txt", silent=FALSE, overwrite=FALSE)

    ## End(Not run)

[Package systemPipeR version 1.22.0 Index]