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Which column one software version reports for each meaning

Description

Answers from the catalogue alone, without data. The rule levels whose version pattern admits the version give the levels; the set’s entries for that pattern give each level’s fields. levels have the slots of a DataCatalog’s levels, holding names: a slot answers one of the set’s keys, such as “normalized_intensity”, with the field’s name, and its $get() takes further qualifiers, such as unit. Lookups that several fields answer, or that an unreviewed level cannot, signal UnresolvedField.

Value

The class generator; Catalog$new() returns a Catalog.

Public fields

levels
One level per rule level, with a DataCatalog’s slots holding names.

Active bindings

description
What this catalogue set holds and who uses it.

Methods

Public methods

Catalog$new()

Bind a catalogue set to the rule levels of one software version.

Usage 
Catalog\$new(software, version, catalog, enforce = NULL)
Arguments
software
The software name, such as “DIA-NN”.
version
The software version, such as “2.2.0”.
catalog
The catalogue set, such as “abundance” or “confidence”; see catalogues().
enforce
NULL, “MUST” or “SHOULD”: signal MissingRequiredField when a field the set requires at that strength is missing.

Catalog$fields()

Every catalogued field the rule declares, one row per field, as catalogue_table() shows them.

Usage 
Catalog\$fields()
Returns

A data frame, with present true for each row.

Catalog$print()

Print the set and the levels.

Usage 
Catalog\$print(...)
Arguments
…
Ignored.

Catalog$clone()

The objects of this class are cloneable with this method.

Usage 
Catalog\$clone(deep = FALSE)
Arguments
deep
Whether to make a deep clone.

Examples

library("apbCatalogR")

catalog <- Catalog$new("DIA-NN", "2.2.0", "abundance")
catalog$levels$peptidoform_ion$layers[["intensity"]]
[1] "Precursor_Quantity"
catalog$levels$peptidoform_ion$layers$keys()
[1] "intensity"                "ms1_intensity"           
[3] "normalized_intensity"     "normalized_ms1_intensity"