type,Workflow-method | R Documentation |
Workflow
class get and set methodsGet and set methods for the Workflow
S4 class.
## 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
x |
S4 object of class |
value |
value to set |
## 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'
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