readComp: Import sample comparisons from targets file

In tgirke/systemPipeR: systemPipeR: workflow management and report generation environment

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 SYSargs2 object
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
args <- loadWorkflow(targets=targets, wf_file="hisat2/hisat2-mapping-se.cwl", 
                  input_file="hisat2/hisat2-mapping-se.yml", dir_path=dir_path)
args <- renderWF(args, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
args
readComp(args, format = "vector", delim = "-")

tgirke/systemPipeR documentation built on March 27, 2024, 11:31 p.m.