RepresentativeMicrohaplotype — RepresentativeMicrohaplotype • pmotoolsr

The representative sequence for a microhaplotype.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

alt_annotations: A list of additional annotations associated with this microhaplotype, e.g. wildtype.
associated_protein_variants: A list of protein variants for this haplotype, e.g. amino acid changes/INDELS.
associated_seq_variants: A list of sequence variants for this haplotype, e.g. SNPS, indels.
masking: Masking info for the sequence.
microhaplotype_name: An optional name for this microhaplotype.
pseudocigar: The pseudocigar of the haplotype.
quality: The ASCII fastq per base quality score for this sequence, this is optional, must be same length as the sequence.
seq: The sequence.
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_annotations: A list of additional annotations associated with this microhaplotype, e.g. wildtype.
associated_protein_variants: A list of protein variants for this haplotype, e.g. amino acid changes/INDELS.
associated_seq_variants: A list of sequence variants for this haplotype, e.g. SNPS, indels.
masking: Masking info for the sequence.
microhaplotype_name: An optional name for this microhaplotype.
pseudocigar: The pseudocigar of the haplotype.
quality: The ASCII fastq per base quality score for this sequence, this is optional, must be same length as the sequence.
seq: The sequence.
extras: Additional properties not explicitly defined in the schema.

Methods

Public methods

RepresentativeMicrohaplotype$new()
RepresentativeMicrohaplotype$validate()
RepresentativeMicrohaplotype$to_list()
RepresentativeMicrohaplotype$to_json_list()
RepresentativeMicrohaplotype$to_json()
RepresentativeMicrohaplotype$clone()

`RepresentativeMicrohaplotype$new()`

Create a new instance.

Usage

RepresentativeMicrohaplotype$new(
  alt_annotations = NULL,
  associated_protein_variants = NULL,
  associated_seq_variants = NULL,
  masking = NULL,
  microhaplotype_name = NULL,
  pseudocigar = NULL,
  quality = NULL,
  seq = NA_character_,
  extras = list()
)

Arguments

alt_annotations: A list of additional annotations associated with this microhaplotype, e.g. wildtype.
associated_protein_variants: A list of protein variants for this haplotype, e.g. amino acid changes/INDELS.
associated_seq_variants: A list of sequence variants for this haplotype, e.g. SNPS, indels.
masking: Masking info for the sequence.
microhaplotype_name: An optional name for this microhaplotype.
pseudocigar: The pseudocigar of the haplotype.
quality: The ASCII fastq per base quality score for this sequence, this is optional, must be same length as the sequence.
seq: The sequence.
extras: Additional properties not explicitly defined in the schema.

`RepresentativeMicrohaplotype$validate()`

Validate the current instance against schema-derived constraints.

Usage

RepresentativeMicrohaplotype$validate()

`RepresentativeMicrohaplotype$to_list()`

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

Usage

RepresentativeMicrohaplotype$to_list()

`RepresentativeMicrohaplotype$to_json_list()`

Convert the object to a JSON-ready R list.

Usage

RepresentativeMicrohaplotype$to_json_list()

`RepresentativeMicrohaplotype$to_json()`

Convert the object to a JSON string.

Usage

RepresentativeMicrohaplotype$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().

`RepresentativeMicrohaplotype$clone()`

The objects of this class are cloneable with this method.

Usage

RepresentativeMicrohaplotype$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.