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PortableMicrohaplotypeObject

PortableMicrohaplotypeObject.Rd

Information on final microhaplotype results from a targeted amplicon analysis with associated meta data.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

  • bioinformatics_methods_info: The bioinformatics pipeline/methods used to generated the microhaplotype analysis for this project.

  • bioinformatics_run_info: The runtime info for the bioinformatics pipeline used to generated the microhaplotypes analysis for this project.

  • detected_microhaplotypes: The microhaplotypes detected in this projects.

  • library_sample_info: A list of libraries of all the seq/amp of the specimens within this PMO file.

  • panel_info: A list of info on the panels.

  • pmo_header: The PMO information for this file including version etc.

  • project_info: The information about the projects stored in this PMO.

  • read_counts_by_stage: The read counts for library_samples for different stages of the pipeline.

  • representative_microhaplotypes: A list of the information on the representative microhaplotypes.

  • sequencing_info: A list of sequencing infos for this PMO file.

  • specimen_info: A list of all the specimens within this PMO file.

  • target_info: A list of info on the targets.

  • targeted_genomes: A list of genomes that any genomic location information refers to.

  • 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

bioinformatics_methods_info

The bioinformatics pipeline/methods used to generated the microhaplotype analysis for this project.

bioinformatics_run_info

The runtime info for the bioinformatics pipeline used to generated the microhaplotypes analysis for this project.

detected_microhaplotypes

The microhaplotypes detected in this projects.

library_sample_info

A list of libraries of all the seq/amp of the specimens within this PMO file.

panel_info

A list of info on the panels.

pmo_header

The PMO information for this file including version etc.

project_info

The information about the projects stored in this PMO.

read_counts_by_stage

The read counts for library_samples for different stages of the pipeline.

representative_microhaplotypes

A list of the information on the representative microhaplotypes.

sequencing_info

A list of sequencing infos for this PMO file.

specimen_info

A list of all the specimens within this PMO file.

target_info

A list of info on the targets.

targeted_genomes

A list of genomes that any genomic location information refers to.

extras

Additional properties not explicitly defined in the schema.

Methods

Public methods

PortableMicrohaplotypeObject$new()

Create a new instance.

Usage

PortableMicrohaplotypeObject$new(
  bioinformatics_methods_info = NULL,
  bioinformatics_run_info = NULL,
  detected_microhaplotypes = list(),
  library_sample_info = list(),
  panel_info = list(),
  pmo_header = NULL,
  project_info = NULL,
  read_counts_by_stage = NULL,
  representative_microhaplotypes = NULL,
  sequencing_info = NULL,
  specimen_info = list(),
  target_info = list(),
  targeted_genomes = NULL,
  extras = list()
)

Arguments

bioinformatics_methods_info

The bioinformatics pipeline/methods used to generated the microhaplotype analysis for this project.

bioinformatics_run_info

The runtime info for the bioinformatics pipeline used to generated the microhaplotypes analysis for this project.

detected_microhaplotypes

The microhaplotypes detected in this projects.

library_sample_info

A list of libraries of all the seq/amp of the specimens within this PMO file.

panel_info

A list of info on the panels.

pmo_header

The PMO information for this file including version etc.

project_info

The information about the projects stored in this PMO.

read_counts_by_stage

The read counts for library_samples for different stages of the pipeline.

representative_microhaplotypes

A list of the information on the representative microhaplotypes.

sequencing_info

A list of sequencing infos for this PMO file.

specimen_info

A list of all the specimens within this PMO file.

target_info

A list of info on the targets.

targeted_genomes

A list of genomes that any genomic location information refers to.

extras

Additional properties not explicitly defined in the schema.

PortableMicrohaplotypeObject$validate()

Validate the current instance against schema-derived constraints.

Usage

PortableMicrohaplotypeObject$validate()

PortableMicrohaplotypeObject$to_list()

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

Usage

PortableMicrohaplotypeObject$to_list()

PortableMicrohaplotypeObject$to_json_list()

Convert the object to a JSON-ready R list.

Usage

PortableMicrohaplotypeObject$to_json_list()

PortableMicrohaplotypeObject$to_json()

Convert the object to a JSON string.

Usage

PortableMicrohaplotypeObject$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().

PortableMicrohaplotypeObject$to_file()

Write this object to a JSON file (compression inferred from the file extension).

Usage

PortableMicrohaplotypeObject$to_file(
  path,
  pretty = FALSE,
  auto_unbox = TRUE,
  validate = TRUE,
  ...
)

Arguments

path

Output file path.

pretty

Logical; pretty-print the JSON.

auto_unbox

Logical; passed to jsonlite::toJSON().

validate

Logical; if TRUE, validate before writing.

...

Additional arguments passed through to write_pmo().

PortableMicrohaplotypeObject$clone()

The objects of this class are cloneable with this method.

Usage

PortableMicrohaplotypeObject$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

pmo <- read_pmo(
  system.file('extdata', 'example_pmo.json.gz', package = 'pmotoolsr'))
length(pmo$specimen_info)
#> [1] 129