defineWorkflow: Define a metabolomics workflow

In jasenfinch/metaboWorkflows: Workflow Project Templates for Metabolomics Analyses

Define a metabolomics workflow

Description

Define a metabolomics data analysis workflow for a given input type and workflow name.

Usage

defineWorkflow(input, workflow, project_name, ...)

## S4 method for signature 'GroverInput'
defineWorkflow(input, workflow, project_name, ...)

## S4 method for signature 'FilePathInput'
defineWorkflow(input, workflow, project_name, ...)

Arguments

input	S4 object of class GroverInput or FilePathInput
workflow	workflow name as returned by availableWorkflows()
project_name	the project name
...	arguments to pass to defineProject. See details.

Details

Further project template options such as the use of the R package renv for R package management can also be declared, which are passed to defineProject(). See the defineProject() documentation for details on these options.

Value

An S4 object of class Workflow

See Also

defineProject()

Examples

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')
workflow_definition

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