systemPipeR (version 1.6.2)

readComp: Import sample comparisons from targets file

Description

Parses sample comparisons specified in 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 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 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.

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 = "-")