readComp: Import sample comparisons from targets file

Description Usage Arguments Value Author(s) Examples

View source: R/utilities.R

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

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
## 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 = "-")

tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.