readComp {systemPipeR} | R Documentation

## Import sample comparisons from targets file

### Description

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'.

### Usage

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

### Arguments

`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`.

### Value

`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.

### Author(s)

Thomas Girke

### Examples

    ## 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 = "-")

[Package systemPipeR version 1.22.0 Index]