LibrarySampleInfo — LibrarySampleInfo • pmotoolsr

Information about a specific amplification and sequencing of a specimen.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

alternate_identifiers: A list of alternative names.
experiment_accession: ERA/SRA experiment accession number for the sample if it was submitted.
fastqs_loc: The location (url or filename path) of the fastqs for a library run.
library_prep_plate_info: Plate location of where library was prepared for sequencing.
library_sample_name: A unique identifier for this sequencing/amplification run.
panel_id: The index into the panel_info list.
qpcr_parasite_density_info: Qpcr parasite density measurement for this extracted sample.
run_accession: ERA/SRA run accession number for the sample if it was submitted.
sequencing_info_id: The index into the sequencing_info list.
specimen_id: The index into the specimen_info list.
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

alternate_identifiers: A list of alternative names.
experiment_accession: ERA/SRA experiment accession number for the sample if it was submitted.
fastqs_loc: The location (url or filename path) of the fastqs for a library run.
library_prep_plate_info: Plate location of where library was prepared for sequencing.
library_sample_name: A unique identifier for this sequencing/amplification run.
panel_id: The index into the panel_info list.
qpcr_parasite_density_info: Qpcr parasite density measurement for this extracted sample.
run_accession: ERA/SRA run accession number for the sample if it was submitted.
sequencing_info_id: The index into the sequencing_info list.
specimen_id: The index into the specimen_info list.
extras: Additional properties not explicitly defined in the schema.

Methods

`LibrarySampleInfo$new()`

Create a new instance.

Usage

LibrarySampleInfo$new(
  alternate_identifiers = NULL,
  experiment_accession = NULL,
  fastqs_loc = NULL,
  library_prep_plate_info = NULL,
  library_sample_name = NA_character_,
  panel_id = NA_real_,
  qpcr_parasite_density_info = NULL,
  run_accession = NULL,
  sequencing_info_id = NULL,
  specimen_id = NA_real_,
  extras = list()
)

Arguments

alternate_identifiers: A list of alternative names.
experiment_accession: ERA/SRA experiment accession number for the sample if it was submitted.
fastqs_loc: The location (url or filename path) of the fastqs for a library run.
library_prep_plate_info: Plate location of where library was prepared for sequencing.
library_sample_name: A unique identifier for this sequencing/amplification run.
panel_id: The index into the panel_info list.
qpcr_parasite_density_info: Qpcr parasite density measurement for this extracted sample.
run_accession: ERA/SRA run accession number for the sample if it was submitted.
sequencing_info_id: The index into the sequencing_info list.
specimen_id: The index into the specimen_info list.
extras: Additional properties not explicitly defined in the schema.

`LibrarySampleInfo$validate()`

Validate the current instance against schema-derived constraints.

Usage

LibrarySampleInfo$validate()

`LibrarySampleInfo$to_list()`

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

Usage

LibrarySampleInfo$to_list()

`LibrarySampleInfo$to_json_list()`

Convert the object to a JSON-ready R list.

Usage

LibrarySampleInfo$to_json_list()

`LibrarySampleInfo$to_json()`

Convert the object to a JSON string.

Usage

LibrarySampleInfo$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().

`LibrarySampleInfo$clone()`

The objects of this class are cloneable with this method.

Usage

LibrarySampleInfo$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.