readComp: Import sample comparisons from targets file
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) Examples

Parses sample comparisons specified in <CMP> line(s) of targets file or in targetsheader slot of SYSargs object. All possible comparisons can be specified with 'CMPset: ALL'.

1	readComp(file, format = "vector", delim = "-")

`file`	Path to targets file. Alternatively, a `SYSargs` or `SYSargs2` object can be assigned.
`format`	Object type to return: `vector` or `matrix`.
`delim`	Delimiter to use when sample comparisons are returned as `vector`.

list where each component is named according to the name(s) used in the <CMP> line(s) of the targets file. The list will contain as many sample comparisons sets (list components) as there are sample comparisons lines in the corresponding targets file.

Thomas Girke

## Return comparisons from targets file
targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
read.delim(targetspath, comment.char = "#")
readComp(file=targetspath, format="vector", delim="-")

## Return comparisons from SYSargs object
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
readComp(args, format = "vector", delim = "-")