R: Write updated targets out to file

writeTargetsout {systemPipeR}

R Documentation

Write updated targets out to file

Description

Convenience write function for generating targets files with updated FileName columns containing the paths to files generated by input/output processes. These processes can be commandline- or R-based software. Typically, the paths to the inputs are stored in the targets infile (targetsin(args)) and the outputs are stored in the targets outfile (targetsout(args)). Note: by default the function cannot overwrite any existing files. If a file exists then the user has to explicitly remove it or set overwrite=TRUE.

Usage

writeTargetsout(x, file = "default", silent = FALSE, overwrite=FALSE, ...)

Arguments

`x`	Object of class `SYSargs`.
`file`	Name and path of output file. If set to "default" then the name of the output file will have the pattern 'targets_<software>.txt', where <software> will be what `software(x)` returns.
`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

Writes tabular targes files containing the header/comment lines from targetsheader(x) and the columns from targetsout(x).

Author(s)

Thomas Girke

Examples

## Create SYSargs object
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)

## Not run: 
## Write targets out file
writeTargetsout(x=args, file="default")

## End(Not run)

[Package systemPipeR version 1.14.0 Index]