MzQCcontrolledVocabulary: A controlled vocabulary document, usually pointing to an .obo...

In rmzqc: Creation, Reading and Validation of 'mzqc' Files

A controlled vocabulary document, usually pointing to an .obo file

Description

A controlled vocabulary document, usually pointing to an .obo file

A controlled vocabulary document, usually pointing to an .obo file

Public fields

name

Full name of the controlled vocabulary.

uri

Publicly accessible URI of the controlled vocabulary.

version

(optional) Version of the controlled vocabulary.

Methods

Public methods

• MzQCcontrolledVocabulary$new()

• MzQCcontrolledVocabulary$isValid()

• MzQCcontrolledVocabulary$toJSON()

• MzQCcontrolledVocabulary$fromData()

• MzQCcontrolledVocabulary$clone()

---

Method new()

Constructor

Usage

MzQCcontrolledVocabulary$new(
  name = NA_character_,
  uri = NA_character_,
  version = NA_character_
)

Arguments

name

String value for initialization of field name

uri

String value for initialization of field uri

version

Optional string value for initialization of field version

---

Method isValid()

Verifies validity of the object

Usage

MzQCcontrolledVocabulary$isValid(context = "MzQCcontrolledVocabulary")

Arguments

context

Optional string describing location in mzQC structure that is used for more informative warning texts.

---

Method toJSON()

Creates JSON file from this object.

Usage

MzQCcontrolledVocabulary$toJSON(...)

Arguments

...

Optional parameters for jsonlite:::asJSON()

---

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCcontrolledVocabulary$fromData(data, context = "MzQCcontrolledVocabulary")

Arguments

data

A datastructure of R lists/arrays as obtained by 'jsonlite::fromJSON()'

context

Optional string describing location in mzQC structure that is used for more informative warning texts.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCcontrolledVocabulary$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  MzQCcontrolledVocabulary$new(
    "Proteomics Standards Initiative Quality Control Ontology",
    "https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.129/psi-ms.obo",
    "4.1.129")

rmzqc documentation built on Aug. 8, 2025, 7:21 p.m.