Workflow-accessors: 'Workflow' class get and set methods

In jasenfinch/metaboWorkflows: Workflow Project Templates for Metabolomics Analyses

Workflow class get and set methods

Description

Get and set methods for the Workflow S4 class.

Usage

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

## S4 replacement method for signature 'Workflow'
type(x) <- value

input(x)

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

input(x) <- value

## S4 replacement method for signature 'Workflow'
input(x) <- value

targets(x)

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

targets(x) <- value

## S4 replacement method for signature 'Workflow'
targets(x) <- value

modules(x)

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

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

## S4 replacement method for signature 'Workflow'
filePaths(x) <- value

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

## S4 replacement method for signature 'Workflow'
sampleInformation(x) <- value

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

## S4 replacement method for signature 'Workflow'
instrument(x) <- value

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

## S4 replacement method for signature 'Workflow'
directory(x) <- value

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

## S4 replacement method for signature 'Workflow'
host(x) <- value

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

## S4 replacement method for signature 'Workflow'
port(x) <- value

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

## S4 replacement method for signature 'Workflow'
auth(x) <- value

Arguments

x	S4 object of class Workflow
value	value to set

Examples

## Define a workflow with file path input
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')

## Return the workflow type
type(workflow_definition)

## Set the workflow type
type(workflow_definition) <- "RP-LC-HRMS profiling" 

## Return the workflow input
input(workflow_definition)

## Set the workflow input
## Not run: 
input(workflow_definition) <- inputGrover(instrument = 'An_instrument',
                                          directory = 'Experiment_directory',
                                          host = 'a.grover.host',
                                          port = 80,
                                          auth = '1234')

## End(Not run)

## Return the workflow targets for the input module
targets(workflow_definition)$input

## Set the workflow targets
targets(workflow_definition) <- list(
                                     a_module = list(
                                     a_target =  target('a_target',
                                                        1 + 1,
                                                        args = list(memory = 'persistent'), 
                                                        comment = 'A target')
                                               )
                                     )

## Return the workflow modules
modules(workflow_definition)

## Return the workflow file paths
## Not run: 
filePaths(workflow_definition)

## End(Not run)

## Set the workflow file paths
filePaths(workflow_definition) <- 'a_file.mzML'

## Return the workflow sample information
sampleInformation(workflow_definition)

## Set the workflow sample information
sampleInformation(workflow_definition) <- tibble::tibble(fileName = 'a_file.mzML')

## Define a workflow with grover input
workflow_input <- inputGrover(instrument = 'An_instrument',
                              directory = 'Experiment_directory',
                              host = 'a.grover.host',
                              port = 80,
                              auth = '1234')

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

## Return the workflow instrument
instrument(workflow_definition)

## Set the workflow Instrument
instrument(workflow_definition) <- 'A_different_instrument'

## Return the workflow directory
directory(workflow_definition)

## Set the workflow directory
directory(workflow_definition) <- 'Another_experiment'

## Return the workflow host
host(workflow_definition)

## Set the workflow_host
host(workflow_definition) <- 'a.new.host'

## Return the workflow port
port(workflow_definition)

## Set the workflow port
port(workflow_definition) <- 81

## Return the workflow auth
auth(workflow_definition)

## Set the workflow auth
auth(workflow_definition) <- 'abcd'

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