writeTargetsRef: Generate targets file with reference

In tgirke/systemPipeR: systemPipeR: workflow management and report generation environment

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)

tgirke/systemPipeR documentation built on March 27, 2024, 11:31 p.m.