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CoreEngine R6 class and methods

Source: R/class_R6_CoreEngine.R
CoreEngine.Rd

The CoreEngine R6 class is a basic data processor with generic methods for handling data.

Note

Removes all results if present in the engine as may be affected but modified correspondence.

Removes all results if present in the engine as may be affected but modified correspondence.

If there are ProcessingSettings objects with the same call names it is better to use run_workflow().

The engine data is saved in an sqlite file and loaded in the app. If save file is defined in the engine it is used, otherwise the save file name is automatically set to the engine class name and the date. Changes made in the app can be saved in the sqlite file and then loaded for scripting.

Public fields

help

(list())
List of function elements to access specific reference help pages.

Active bindings

headers

List of project headers.

settings

List of processing settings.

history

Audit trail of changes.

analyses

List of analyses.

results

List of results.

save_file

Full path to the save file of the engine data.

Methods

Public methods

Method new()

Creates an R6 CoreEngine class object.

Usage

CoreEngine$new(
  headers = NULL,
  settings = NULL,
  analyses = NULL,
  results = NULL
)

Arguments

headers

A named list with headers or a ProjectHeaders S3 class object. Each list element must have length one. There is no type restrictions except for name (must be type character length 1), author (must be type character length 1), file (must be type character length 1) and date (must be class POSIXct or class POSIXt length 1). See more information in ?ProjectHeaders.

settings

A named list of ProcessingSettings objects or a single ProcessingSettings object. The list names should match the call name of each ProcessingSettings object. Alternatively, a named list with call name, algorithm and parameters to be transformed and added as ProcessingSettings object.

analyses

An Analysis S3 class object or a list with Analysis S3 class objects as elements (see ?Analysis for more information).

results

A named list of objects from processing methods.

Method print()

Prints a summary to the console.

Usage

CoreEngine$print()

Method print_headers()

Prints the headers list.

Usage

CoreEngine$print_headers()

Method print_analyses()

Prints the analyses.

Usage

CoreEngine$print_analyses()

Method print_workflow()

Prints the order of processing methods for all added processing settings.

Usage

CoreEngine$print_workflow()

Method print_results()

Prints the data results added to the engine.

Usage

CoreEngine$print_results()

Method get_headers()

Gets the headers list.

Usage

CoreEngine$get_headers(value = NULL)

Arguments

value

A character vector with the name/s of the header elements. When NULL (the default), the entire headers list is returned.

Method get_history()

Gets the object history (audit trail) as a data.table.

Usage

CoreEngine$get_history()

Method get_analyses()

Gets the list of analyses.

Usage

CoreEngine$get_analyses(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_number_analyses()

Gets the number of analyses.

Usage

CoreEngine$get_number_analyses()

Method get_overview()

Gets an overview data.table with all the analysis names,replicates, associated blank replicates, and full file paths.

Usage

CoreEngine$get_overview()

Method get_analysis_names()

Gets the analysis names.

Usage

CoreEngine$get_analysis_names(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_replicate_names()

Gets the analysis replicate names.

Usage

CoreEngine$get_replicate_names(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_blank_names()

Gets the analysis blank replicate names.

Usage

CoreEngine$get_blank_names(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_files()

Gets the full file paths of each analysis.

Usage

CoreEngine$get_files(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_formats()

Gets the file format of each analysis.'

Usage

CoreEngine$get_formats(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_types()

Gets the type of each analysis.

Usage

CoreEngine$get_types(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method get_settings()

Gets the processing settings list.

Usage

CoreEngine$get_settings(call = NULL)

Arguments

call

A string or a vector of strings with the name/s of the processing method/s.

Method get_settings_names()

Gets the call names of all processing methods in added processing settings as a character vector.

Usage

CoreEngine$get_settings_names()

Method get_workflow_overview()

A data.table with the overview of all processing methods from added processing settings.

Usage

CoreEngine$get_workflow_overview()

Method get_results_names()

Gets names of present results data.

Usage

CoreEngine$get_results_names()

Method get_results()

Gets the list of results data.

Usage

CoreEngine$get_results(results = NULL)

Arguments

results

A character vector with the name of the module/s.

Method add_headers()

Adds headers. If an argument or element "name" is given, it must be type character. If an argument or element path is given, it must be type character and exist. If an argument or element date is given, it must be class POSIXct or POSIXt. If given date is character, conversion to class POSIXct or POSIXt is attempted. See ?ProjectHeaders for more information.

Usage

CoreEngine$add_headers(...)

Arguments

...

Arguments to be added as headers. Note that all given arguments must be of length one. There is no type limitations. The name of the argument becomes the name of the header entry. Alternatively, a single list argument with the headers (all length one) can be given.

Returns

Invisible.

Method add_settings()

Adds processing settings.

Usage

CoreEngine$add_settings(settings = NULL, replace = FALSE)

Arguments

settings

A named list of ProcessingSettings objects or a single ProcessingSettings object. The list names should match the call name of each ProcessingSettings object. Alternatively, a named list with call name, algorithm and parameters to be transformed and added as ProcessingSettings object.

replace

Logical of length one. When TRUE, existing settings are replaced by the new settings with the same call name, except settings for methods that can be applied more than once. The default is FALSE.

Returns

Invisible.

Method add_analyses()

Adds analyses.

Usage

CoreEngine$add_analyses(analyses = NULL)

Arguments

analyses

An Analysis S3 class object or a list with Analysis S3 objects as elements.

Returns

Invisible.

Method add_replicate_names()

Adds or redefines the analysis replicate names.

Usage

CoreEngine$add_replicate_names(value = NULL)

Arguments

value

A character vector with the analysis replicate names. Must be of the same length as the number of analyses.

Method add_blank_names()

Adds or redefines the analysis blank replicate names.

Usage

CoreEngine$add_blank_names(value = NULL)

Arguments

value

A character vector with the analysis blank replicate names. Must be of the same length as the number of analyses.

Method add_metadata()

Adds metadata to analyses.

Usage

CoreEngine$add_metadata(value = NULL)

Arguments

value

A data.frame or data.table with metadata for the analyses. The data.frame or data.table must have an analysis column and the same number of rows as the number of analyses in the engine. Metadata is added using any extra columns of the data.frame or data.table.

Returns

Invisible.

Method add_results()

Adds data from results to the engine.

Usage

CoreEngine$add_results(value = NULL)

Arguments

value

A named list with data from results.

Returns

Invisible.

Method remove_headers()

Removes headers entries. Note that the name, path and date headers cannot be removed only changed.

Usage

CoreEngine$remove_headers(value = NULL)

Arguments

value

A character vector with the name/s of the elements in headers to be removed.

Returns

Invisible.

Method remove_settings()

Removes settings.

Usage

CoreEngine$remove_settings(call = NULL)

Arguments

call

A string or a vector of strings with the name/s of the processing method/s to be removed. Alternatively, an integer vector with the index/es of the settings to be removed. When call is NULL all settings are removed.

Returns

Invisible.

Method remove_analyses()

Removes analyses.

Usage

CoreEngine$remove_analyses(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Returns

Invisible.

Method remove_results()

Removes results data.

Usage

CoreEngine$remove_results(results)

Arguments

results

A named list of objects from processing methods.

Returns

Invisible.

Method subset_analyses()

Subsets on analyses returning a new cloned object with only the analyses to keep.

Usage

CoreEngine$subset_analyses(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Method has_settings()

Checks if there are processing settings, returning TRUE or FALSE.

Usage

CoreEngine$has_settings(call = NULL)

Arguments

call

A string or a vector of strings with the name/s of the processing method/s.

Method has_analyses()

Checks if analyses are present, returning TRUE or FALSE.

Usage

CoreEngine$has_analyses()

Method has_results()

Checks if results are present, returning TRUE or FALSE.

Usage

CoreEngine$has_results(names = NULL)

Arguments

names

A string or a vector of strings with the name/s of the results data. The actual names depends of the applied algorithms. For instance, when algorithms via patRoon are used, the name of the module data is patRoon.

Method process()

Runs a processing method with the provided settings.

Usage

CoreEngine$process(settings = NULL)

Arguments

settings

A ProcessingSettings object or a character string with the call name of a previously added ProcessingSettings in the engine.

Method run_workflow()

Runs all processing results represented by added processing settings.

Usage

CoreEngine$run_workflow()

Returns

Invisible.

Method save()

Saves the engine data as sqlite file.

Usage

CoreEngine$save(file = NA_character_)

Arguments

file

A string with the full file path of the sqlite file. If NA (the default) and no file header is defined in the engine, the file name is automatically created with the engine class name and the date.

Method load()

Loads the engine data from an sqlite file.

Usage

CoreEngine$load(file = NA_character_)

Arguments

file

A string with the full file path of the sqlite file. If NA (the default) and no file header is defined in the engine, the file name is automatically created with the engine class name and the date.

Method export_headers()

Exports the headers as json (the default) or rds.

Usage

CoreEngine$export_headers(format = "json", name = "headers", path = getwd())

Arguments

format

A string. Possible values are json and rds for saving as JSON or RDS formats, respectively.

name

String with the name of the file to be saved.

path

String with the directory of the file to be saved.

Method export_settings()

Exports the settings as json (the default) or rds.

Usage

CoreEngine$export_settings(
  call = NULL,
  format = "json",
  name = "settings",
  path = getwd()
)

Arguments

call

A string or a vector of strings with the name/s of the processing method/s to be exported. When call is NULL all settings are saved.

format

A string. Possible values are json and rds for saving as JSON or RDS formats, respectively.

name

String with the name of the file to be saved.

path

String with the directory of the file to be saved.

Method export_analyses()

Exports the analyses as json (the default) or rds.

Usage

CoreEngine$export_analyses(
  analyses = NULL,
  format = "json",
  name = "analyses",
  path = getwd()
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

format

A string. Possible values are json and rds for saving as JSON or RDS formats, respectively.

name

String with the name of the file to be saved.

path

String with the directory of the file to be saved.

Method export()

Exports the engine data as as json (the default) or rds.

Usage

CoreEngine$export(format = "json", name = "EngineData", path = getwd())

Arguments

format

A string. Possible values are json and rds for saving as JSON or RDS formats, respectively.

name

String with the name of the file to be saved.

path

String with the directory of the file to be saved.

Method import_headers()

Imports headers from an rds or json file.

Usage

CoreEngine$import_headers(file = NA_character_)

Arguments

file

A json or rds file to be imported.

Returns

Invisible.

Method import_settings()

Imports settings from an rds or json file.

Usage

CoreEngine$import_settings(file = NA_character_, replace = TRUE)

Arguments

file

A json or rds file to be imported.

replace

Logical. When TRUE, existing settings are replaced by the new settings with the same call name.

Method import_analyses()

Imports analyses from an rds or json file.

Usage

CoreEngine$import_analyses(file = NA_character_)

Arguments

file

A json or rds file to be imported.

Method import()

Imports a CoreEngine saved as json or rds.

Usage

CoreEngine$import(file = NA_character_)

Arguments

file

A json or rds file representing a CoreEngine.

Returns

Invisible.

Method run_app()

Runs a Shiny app to explore and manage the engine.

Usage

CoreEngine$run_app()

Method processing_methods()

Data.table with available data processing methods.

Usage

CoreEngine$processing_methods()

Method clone()

The objects of this class are cloneable with this method.

Usage

CoreEngine$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.