rmzqc (version 0.7.0)

MzQCbaseQuality: Base class of runQuality/setQuality

Description

Base class of runQuality/setQuality

Base class of runQuality/setQuality

Public fields

metadata

The metadata for this run/setQuality

qualityMetrics

Array of MzQCqualityMetric objects

Methods

Public methods

• MzQCbaseQuality$new()

• MzQCbaseQuality$isValid()

• MzQCbaseQuality$getMetric()

• MzQCbaseQuality$toJSON()

• MzQCbaseQuality$fromData()

• MzQCbaseQuality$clone()

---

Method new()

Constructor

Usage

MzQCbaseQuality$new(metadata = MzQCmetadata$new(), qualityMetrics = list())

Arguments

metadata

Optional MzQCmetadata value for initialization of field metadata

qualityMetrics

Optional list value for initialization of field qualityMetrics

---

Method isValid()

Verifies validity of the object

Usage

MzQCbaseQuality$isValid(context = "MzQCbaseQuality")

Arguments

context

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

---

Method getMetric()

Fetches metrics which match specified accession or name from the object.

Usage

MzQCbaseQuality$getMetric(accession = NULL, name = NULL)

Arguments

accession

Search by accession

name

Search by name

---

Method toJSON()

Creates JSON file from this object.

Usage

MzQCbaseQuality$toJSON(...)

Arguments

...

Optional parameters for jsonlite:::asJSON()

---

Method fromData()

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

Usage

MzQCbaseQuality$fromData(mdata, context = "MzQCbaseQuality")

Arguments

mdata

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

MzQCbaseQuality$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.