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SequencingInfo

SequencingInfo.Rd

Information on sequencing info.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

  • library_kit: Name, version, and applicable cell or cycle numbers for the kit used to prepare libraries and load cells or chips for sequencing. If possible, include a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001.

  • library_layout: Specify the configuration of reads, e.g. paired-end, single.

  • library_screen: Describe enrichment, screening, or normalization methods applied during amplification or library preparation, e.g. size selection 390bp, diluted to 1 ng DNA/sample.

  • library_selection: How amplification was done (common are PCR=Source material was selected by designed primers, RANDOM =Random selection by shearing or other method).

  • library_source: Source of amplification material e.g. was it DNA (GENOMIC) or RNA (TRANSCRIPTOMIC) (common names GENOMIC, TRANSCRIPTOMIC).

  • library_strategy: What the nuceloacid sequencing/amplification strategy was (common names are AMPLICON, WGS).

  • nucl_acid_amp: Link to a reference or kit that describes the enzymatic amplification of nucleic acids.

  • nucl_acid_amp_date: The date of the nucleoacid amplification.

  • nucl_acid_ext: Link to a reference or kit that describes the recovery of nucleic acids from the sample.

  • nucl_acid_ext_date: The date of the nucleoacid extraction.

  • pcr_cond: The method/conditions for PCR, List PCR cycles used to amplify the target.

  • seq_center: Name of facility where sequencing was performed (lab, core facility, or company).

  • seq_date: The date of sequencing, should be YYYY-MM or YYYY-MM-DD.

  • seq_instrument_model: The sequencing instrument model used to sequence the run, e.g. NextSeq 2000, MinION, Revio.

  • seq_platform: The sequencing technology used to sequence the run, e.g. ILLUMINA, NANOPORE, PACBIO.

  • sequencing_info_name: A name for a specific sequencing run, e.g. batch1.

  • 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

library_kit

Name, version, and applicable cell or cycle numbers for the kit used to prepare libraries and load cells or chips for sequencing. If possible, include a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001.

library_layout

Specify the configuration of reads, e.g. paired-end, single.

library_screen

Describe enrichment, screening, or normalization methods applied during amplification or library preparation, e.g. size selection 390bp, diluted to 1 ng DNA/sample.

library_selection

How amplification was done (common are PCR=Source material was selected by designed primers, RANDOM =Random selection by shearing or other method).

library_source

Source of amplification material e.g. was it DNA (GENOMIC) or RNA (TRANSCRIPTOMIC) (common names GENOMIC, TRANSCRIPTOMIC).

library_strategy

What the nuceloacid sequencing/amplification strategy was (common names are AMPLICON, WGS).

nucl_acid_amp

Link to a reference or kit that describes the enzymatic amplification of nucleic acids.

nucl_acid_amp_date

The date of the nucleoacid amplification.

nucl_acid_ext

Link to a reference or kit that describes the recovery of nucleic acids from the sample.

nucl_acid_ext_date

The date of the nucleoacid extraction.

pcr_cond

The method/conditions for PCR, List PCR cycles used to amplify the target.

seq_center

Name of facility where sequencing was performed (lab, core facility, or company).

seq_date

The date of sequencing, should be YYYY-MM or YYYY-MM-DD.

seq_instrument_model

The sequencing instrument model used to sequence the run, e.g. NextSeq 2000, MinION, Revio.

seq_platform

The sequencing technology used to sequence the run, e.g. ILLUMINA, NANOPORE, PACBIO.

sequencing_info_name

A name for a specific sequencing run, e.g. batch1.

extras

Additional properties not explicitly defined in the schema.

Methods

Public methods

SequencingInfo$new()

Create a new instance.

Usage

SequencingInfo$new(
  library_kit = NULL,
  library_layout = NA_character_,
  library_screen = NULL,
  library_selection = NA_character_,
  library_source = NA_character_,
  library_strategy = NA_character_,
  nucl_acid_amp = NULL,
  nucl_acid_amp_date = NULL,
  nucl_acid_ext = NULL,
  nucl_acid_ext_date = NULL,
  pcr_cond = NULL,
  seq_center = NULL,
  seq_date = NULL,
  seq_instrument_model = NA_character_,
  seq_platform = NA_character_,
  sequencing_info_name = NA_character_,
  extras = list()
)

Arguments

library_kit

Name, version, and applicable cell or cycle numbers for the kit used to prepare libraries and load cells or chips for sequencing. If possible, include a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001.

library_layout

Specify the configuration of reads, e.g. paired-end, single.

library_screen

Describe enrichment, screening, or normalization methods applied during amplification or library preparation, e.g. size selection 390bp, diluted to 1 ng DNA/sample.

library_selection

How amplification was done (common are PCR=Source material was selected by designed primers, RANDOM =Random selection by shearing or other method).

library_source

Source of amplification material e.g. was it DNA (GENOMIC) or RNA (TRANSCRIPTOMIC) (common names GENOMIC, TRANSCRIPTOMIC).

library_strategy

What the nuceloacid sequencing/amplification strategy was (common names are AMPLICON, WGS).

nucl_acid_amp

Link to a reference or kit that describes the enzymatic amplification of nucleic acids.

nucl_acid_amp_date

The date of the nucleoacid amplification.

nucl_acid_ext

Link to a reference or kit that describes the recovery of nucleic acids from the sample.

nucl_acid_ext_date

The date of the nucleoacid extraction.

pcr_cond

The method/conditions for PCR, List PCR cycles used to amplify the target.

seq_center

Name of facility where sequencing was performed (lab, core facility, or company).

seq_date

The date of sequencing, should be YYYY-MM or YYYY-MM-DD.

seq_instrument_model

The sequencing instrument model used to sequence the run, e.g. NextSeq 2000, MinION, Revio.

seq_platform

The sequencing technology used to sequence the run, e.g. ILLUMINA, NANOPORE, PACBIO.

sequencing_info_name

A name for a specific sequencing run, e.g. batch1.

extras

Additional properties not explicitly defined in the schema.

SequencingInfo$validate()

Validate the current instance against schema-derived constraints.

Usage

SequencingInfo$validate()

SequencingInfo$to_list()

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

Usage

SequencingInfo$to_list()

SequencingInfo$to_json_list()

Convert the object to a JSON-ready R list.

Usage

SequencingInfo$to_json_list()

SequencingInfo$to_json()

Convert the object to a JSON string.

Usage

SequencingInfo$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().

SequencingInfo$clone()

The objects of this class are cloneable with this method.

Usage

SequencingInfo$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.