writeTargetsRef: Generate targets file with reference
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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.

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.

Thomas Girke

writeTargetsout, mergeBamByFactor

## 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)