MzQCinputFile: An inputfile within metadata for a run/setQuality

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

An inputfile within metadata for a run/setQuality

Description

An inputfile within metadata for a run/setQuality

An inputfile within metadata for a run/setQuality

Public fields

name

The name MUST uniquely match to a location (specified below) listed in the mzQC file.

location

Unique file location, REQUIRED to be specified as a URI. The file URI is RECOMMENDED to be publicly accessible.

fileFormat

An MzQCcvParameter with 'accession' and 'name'.

fileProperties

An array of MzQCcvParameter, usually with 'accession', 'name' and 'value'. Recommended are at least two entries: a) Completion time of the input file (MS:1000747) and b) Checksum of the input file (any child of: MS:1000561 ! data file checksum type).

Methods

Public methods

• MzQCinputFile$new()

• MzQCinputFile$isValid()

• MzQCinputFile$toJSON()

• MzQCinputFile$fromData()

• MzQCinputFile$clone()

---

Method new()

Constructor

Usage

MzQCinputFile$new(
  name = NA_character_,
  location = NA_character_,
  fileFormat = MzQCcvParameter$new(),
  fileProperties = list()
)

Arguments

name

String value for initialization of field name

location

String value for initialization of field location

fileFormat

Optional MzQCcvParameter value for initialization of field fileFormat

fileProperties

Optional list value for initialization of field fileProperties

---

Method isValid()

Verifies validity of the object

Usage

MzQCinputFile$isValid(context = "MzQCinputFile")

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

MzQCinputFile$toJSON(...)

Arguments

...

Optional parameters for jsonlite:::asJSON()

---

Method fromData()

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

Usage

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

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

MzQCinputFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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