GenomeInfo — GenomeInfo • pmotoolsr

Information on a genome.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

chromosomes: A list of the chromosomes/contigs found within this genome.
genome_version: The genome version.
gff_url: A link to the where this genome's annotation file could be downloaded.
name: Name of the genome.
taxon_id: The NCBI taxonomy number, can be a list of values if it's a genome file that has been created by combining gnomes from different species.
url: A link to the where this genome file could be downloaded.
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

chromosomes: A list of the chromosomes/contigs found within this genome.
genome_version: The genome version.
gff_url: A link to the where this genome's annotation file could be downloaded.
name: Name of the genome.
taxon_id: The NCBI taxonomy number, can be a list of values if it's a genome file that has been created by combining gnomes from different species.
url: A link to the where this genome file could be downloaded.
extras: Additional properties not explicitly defined in the schema.

Methods

`GenomeInfo$new()`

Create a new instance.

Usage

GenomeInfo$new(
  chromosomes = NULL,
  genome_version = NA_character_,
  gff_url = NULL,
  name = NA_character_,
  taxon_id = numeric(),
  url = NA_character_,
  extras = list()
)

Arguments

chromosomes: A list of the chromosomes/contigs found within this genome.
genome_version: The genome version.
gff_url: A link to the where this genome's annotation file could be downloaded.
name: Name of the genome.
taxon_id: The NCBI taxonomy number, can be a list of values if it's a genome file that has been created by combining gnomes from different species.
url: A link to the where this genome file could be downloaded.
extras: Additional properties not explicitly defined in the schema.

`GenomeInfo$validate()`

Validate the current instance against schema-derived constraints.

Usage

GenomeInfo$validate()

`GenomeInfo$to_list()`

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

Usage

GenomeInfo$to_list()

`GenomeInfo$to_json_list()`

Convert the object to a JSON-ready R list.

Usage

GenomeInfo$to_json_list()

`GenomeInfo$to_json()`

Convert the object to a JSON string.

Usage

GenomeInfo$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().

`GenomeInfo$clone()`

The objects of this class are cloneable with this method.

Usage

GenomeInfo$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.