FeaturesOfInterest-class {MSnbase} | R Documentation

## Features of Interest

### Description

The Features of Interest infrastructure allows to define a set of features of particular interest to be used/matched against existing data sets contained in `"MSnSet"`. A specific set of features is stored as an `FeaturesOfInterest` object and a collection of such non-redundant instances (for example for a specific organism, project, ...) can be collected in a `FoICollection`.

### Objects from the Class

Objects can be created with the respective `FeaturesOfInterest` and `FoICollection` constructors.

`FeaturesOfInterest` instances can be generated in two different ways: the constructor takes either (1) a set of features names (a `character` vector) and a description (`character` of length 1 - any subsequent elements are silently ignored) or (2) feature names, a description and an instance of class `"MSnSet"`. In the latter case, we call such `FeaturesOfInterest` objects traceable, because we can identify the origin of the feature names and thus their validity. This is done by inspecting the `MSnSet` instance and recording its dimensions, its name and a unique md5 hash tag (these are stores as part of the optional `objpar` slot). In such cases, the feature names passed to the `FeaturesOfInterest` constructor must also be present in the `MSnSet`; if one or more are not, an error will be thrown. If your features of interest to be recorded stem for an existing experiment and have all been observed, it is advised to pass the 3 arguments to the constructor to ensure that the feature names as valid. Otherwise, only the third argument should be omitted.

`FoICollection` instances can be constructed by creating an empty collection and serial additions of `FeaturesOfInterest` using `addFeaturesOfInterest` or by passing a list of `FeaturesOfInterest` instance.

### Slots

`FeaturesOfInterest` class:

`description`:

  Object of class `"character"` describing the instance.

`objpar`:

  Optional object of class `"list"` providing details about the `MSnSet` instance originally used to create the instance. See details section.

`fnames`:

  Object of class `"character"` with the feature of interest names.

`date`:

  Object of class `"character"` with the date the instance was first generated.

`.__classVersion__`:

  Object of class `"Versions"` with the `FeaturesOfInterest` class version. Only relevant for development.

`FoICollection` class:

`foic`:

  Object of class `"list"` with the `FeaturesOfInterest`.

`.__classVersion__`:

  Object of class `"Versions"` with the `FoICollection` class version. Only relevant for development.

### Extends

Class `"Versioned"`, directly.

### Methods

`FeaturesOfInterest` class:

description

  `signature(object = "FeaturesOfInterest")`: returns the description of `object`.

foi

  `signature(object = "FeaturesOfInterest")`: returns the features of interests.

length

  `signature(x = "FeaturesOfInterest")`: returns the number of features of interest in `x`.

show

  `signature(object = "FeaturesOfInterest")`: displays `object`.

fnamesIn

  `signature(x = "FeaturesOfInterst", y = "MSnSet", count = "logical")`: if `count` is `FALSE` (default), return a logical indicating whether there is at least one feautre of interest present in `x`? Otherwise, returns the number of such features. Works also with matrices and data.frames.

[

  Subsetting works like lists. Returns a new `FoICollection`.

[[

  Subsetting works like lists. Returns a new `FeatureOfInterest`.

`FoICollection` class:

description

  `signature(object = "FoICollection")`: returns the description of `object`.

foi

  `signature(object = "FoICollection")`: returns a list of `FeaturesOfInterest`.

length

  `signature(x = "FoICollection")`: returns the number of `FeaturesOfInterest` in the collection.

lengths

  `signature(x = "FoICollection")`: returns the number of features of interest in each `FeaturesOfInterest` in the collection `x`.

addFeaturesOfInterest

  `signature(x = "FeaturesOfInterest", y = "FoICollection")`: add the `FeaturesOfInterest` instance `x` to `FoICollection` `y`. If `x` is already present, a message is printed and `y` is returned unchanged.

rmFeaturesOfInterest

  `signature(object = "FoICollection", i = "numeric")`: removes the `i`th `FeatureOfInterest` in the collection `object`.

show

  `signature(object = "FoICollection")`: displays `object`.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### Examples

    library("pRolocdata")
    data(tan2009r1)

    x <- FeaturesOfInterest(description = "A traceable test set of features of interest",
                            fnames = featureNames(tan2009r1)[1:10],
                            object = tan2009r1)
    x

    description(x)
    foi(x)

    y <- FeaturesOfInterest(description = "Non-traceable features of interest",
                            fnames = featureNames(tan2009r1)[111:113])
    y

    ## an illegal FeaturesOfInterest
    try(FeaturesOfInterest(description = "Won't work",
                           fnames = c("A", "Z", featureNames(tan2009r1)),
                           object = tan2009r1))

    FeaturesOfInterest(description = "This work, but not traceable",
                           fnames = c("A", "Z", featureNames(tan2009r1)))

    xx <- FoICollection()
    xx

    xx <- addFeaturesOfInterest(x, xx)
    xx <- addFeaturesOfInterest(y, xx)
    names(xx) <- LETTERS[1:2]
    xx

    ## Sub-setting
    xx[1]
    xx[[1]]
    xx[["A"]]

    description(xx)
    foi(xx)

    fnamesIn(x, tan2009r1)
    fnamesIn(x, tan2009r1, count = TRUE)

    rmFeaturesOfInterest(xx, 1)

[Package MSnbase version 2.12.0 Index]