GenomicLocation — GenomicLocation • pmotoolsr

Information on the genomic location of specific sequence.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

alt_seq: A possible alternative sequence of this genomic location.
chrom: The chromosome name.
end: The end of the location, 0-based positioning.
genome_id: The index to the genome in the targeted_genomes list that this location refers to.
ref_seq: The reference sequence of this genomic location.
start: The start of the location, 0-based positioning.
strand: Which strand the location is, either + for plus strand or - for negative strand.
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

alt_seq: A possible alternative sequence of this genomic location.
chrom: The chromosome name.
end: The end of the location, 0-based positioning.
genome_id: The index to the genome in the targeted_genomes list that this location refers to.
ref_seq: The reference sequence of this genomic location.
start: The start of the location, 0-based positioning.
strand: Which strand the location is, either + for plus strand or - for negative strand.
extras: Additional properties not explicitly defined in the schema.

Methods

`GenomicLocation$new()`

Create a new instance.

Usage

GenomicLocation$new(
  alt_seq = NULL,
  chrom = NA_character_,
  end = NA_real_,
  genome_id = NA_real_,
  ref_seq = NULL,
  start = NA_real_,
  strand = NULL,
  extras = list()
)

Arguments

alt_seq: A possible alternative sequence of this genomic location.
chrom: The chromosome name.
end: The end of the location, 0-based positioning.
genome_id: The index to the genome in the targeted_genomes list that this location refers to.
ref_seq: The reference sequence of this genomic location.
start: The start of the location, 0-based positioning.
strand: Which strand the location is, either + for plus strand or - for negative strand.
extras: Additional properties not explicitly defined in the schema.

`GenomicLocation$validate()`

Validate the current instance against schema-derived constraints.

Usage

GenomicLocation$validate()

`GenomicLocation$to_list()`

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

Usage

GenomicLocation$to_list()

`GenomicLocation$to_json_list()`

Convert the object to a JSON-ready R list.

Usage

GenomicLocation$to_json_list()

`GenomicLocation$to_json()`

Convert the object to a JSON string.

Usage

GenomicLocation$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().

`GenomicLocation$clone()`

The objects of this class are cloneable with this method.

Usage

GenomicLocation$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.