targetsWorkflow: Workflow pipeline targets

In jasenfinch/metaboWorkflows: Workflow Project Templates for Metabolomics Analyses

Workflow pipeline targets

Description

Target definitions for workflow input.

Usage

targetsWorkflow(x)

## S4 method for signature 'Workflow'
targetsWorkflow(x)

targetsInput(x)

## S4 method for signature 'FilePathInput'
targetsInput(x)

## S4 method for signature 'GroverInput'
targetsInput(x)

## S4 method for signature 'Workflow'
targetsInput(x)

targetsSpectralProcessing(x)

targetsPretreatment(x)

targetsMFassignment(x)

targetsModelling(x)

targetsCorrelations(x)

targetsReport(x, project_directory)

Arguments

x	the workflow type or an S4 object of class Workflow, FilePathInput or GroverInput
project_directory	the path of the project directory

Value

A list of Target S4 class target definitions.

Examples

## Full workflow example
file_paths <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
sample_information <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')

workflow_input <- inputFilePath(file_paths,sample_information)

workflow_definition <- defineWorkflow(workflow_input,
                                     'FIE-HRMS fingerprinting',
                                     'Example project')

targetsWorkflow(workflow_definition)

## Examples for individual modules
targetsSpectralProcessing('FIE-HRMS fingerprinting')
targetsInput(workflow_input)
targetsPretreatment('FIE-HRMS fingerprinting')
targetsMFassignment('FIE-HRMS fingerprinting')
targetsModelling('FIE-HRMS fingerprinting')
targetsCorrelations('FIE-HRMS fingerprinting')

jasenfinch/metaboWorkflows documentation built on May 24, 2023, 8:23 a.m.