BioMethod

Bioinformatics methodology description with info on program, version, and arguments different from the default.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

• additional_argument: Any additional arguments that differ from the default arguments.

• program: Name of the program used for this portion of the pipeline.

• program_description: A short description of what this method does.

• program_url: A url pointing to code base of a program, e.g. a github link.

• program_version: The version of program, should be in the format of v[MAJOR].[MINOR].[PATCH].

• extras: Additional properties not explicitly defined in the schema.

Methods

See inline method documentation for initialize(), validate(), to_list(), to_json_list(), and to_json().

Public fields

additional_argument

Any additional arguments that differ from the default arguments.

program

Name of the program used for this portion of the pipeline.

program_description

A short description of what this method does.

program_url

A url pointing to code base of a program, e.g. a github link.

program_version

The version of program, should be in the format of v[MAJOR].[MINOR].[PATCH].

extras

Additional properties not explicitly defined in the schema.

Methods

Public methods

• BioMethod$new()

• BioMethod$validate()

• BioMethod$to_list()

• BioMethod$to_json_list()

• BioMethod$to_json()

• BioMethod$clone()

---

BioMethod$new()

Create a new instance.

Usage

BioMethod$new(
  additional_argument = NULL,
  program = NA_character_,
  program_description = NULL,
  program_url = NULL,
  program_version = NA_character_,
  extras = list()
)

Arguments

additional_argument

Any additional arguments that differ from the default arguments.

program

Name of the program used for this portion of the pipeline.

program_description

A short description of what this method does.

program_url

A url pointing to code base of a program, e.g. a github link.

program_version

The version of program, should be in the format of v[MAJOR].[MINOR].[PATCH].

extras

Additional properties not explicitly defined in the schema.

---

BioMethod$validate()

Validate the current instance against schema-derived constraints.

Usage

BioMethod$validate()

---

BioMethod$to_list()

Convert the object to a plain R list using in-memory values.

Usage

BioMethod$to_list()

---

BioMethod$to_json_list()

Convert the object to a JSON-ready R list.

Usage

BioMethod$to_json_list()

---

BioMethod$to_json()

Convert the object to a JSON string.

Usage

BioMethod$to_json(pretty = FALSE, auto_unbox = TRUE, ...)

Arguments

pretty

Logical; pretty-print the JSON.

auto_unbox

Logical; passed to jsonlite::toJSON().

...

Additional arguments passed to jsonlite::toJSON().

---

BioMethod$clone()

The objects of this class are cloneable with this method.

Usage

BioMethod$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.