QFeatures-type: Set and Get QFeatures Type
In lgatto/Features: Quantitative features for mass spectrometry data

setQFeaturesType

R Documentation

Set and Get QFeatures Type

Description

Developer-level functions to set and retrieve the type of a QFeatures object. This type can help internal methods adapt their behaviour to the structure of the data.

Usage

setQFeaturesType(object, type)

getQFeaturesType(object)

validQFeaturesTypes()

Arguments

`object`	An instance of class QFeatures.
`type`	`character(1)` defining the type of the QFeatures. Must be one of the values returned by `validQFeaturesTypes()`.

Details

These functions control an internal metadata slot (._type) used to distinguish between different structural uses of QFeatures objects. This slot is directly accessible with metadata(object)[["._type"]].

Value

setQFeaturesType(): returns the updated QFeatures object with the type stored in its metadata.
getQFeaturesType(): returns a character string indicating the type of the QFeatures object. If no type is explicitly set, it is inferred from the class of the experiments. If the QFeatures contains any SingleCellExperiment objects, the type is set to "scp". Otherwise, it is set to "bulk".
validQFeaturesTypes(): character vector of valid QFeatures types.

Warning

These functions are intended for package developers and internal use. End users should typically not call them directly.

Note

The QFeatures type slot was introduced because, in the context of the scp package, we found that SingleCellExperiment objects were slower than SummarizedExperiment objects (GH issue: scp#83). As a result, we started using SummarizedExperiment objects within scp. However, to retain information about the type of data being handled, we introduced the QFeatures type slot. This slot is, for example, used in the show method of QFeatures.