Features of Interest — FeaturesOfInterest-class • MSnbase

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 ith FeatureOfInterest in the collection object.
show: signature(object = "FoICollection"): displays object.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(tan2009r1)

x <- FeaturesOfInterest(description = "A traceable test set of features of interest",
                        fnames = featureNames(tan2009r1)[1:10],
                        object = tan2009r1)
x
#> Traceable object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   A traceable test set of features of interest
#>  10 features of interest:
#>    P20353, P53501  ...  Q9VCK0, Q9VIU7

description(x)
#> [1] "A traceable test set of features of interest"
foi(x)
#>  [1] "P20353" "P53501" "Q7KU78" "P04412" "Q7KJ73" "Q7JZN0" "Q7KLV9" "Q9VM65"
#>  [9] "Q9VCK0" "Q9VIU7"

y <- FeaturesOfInterest(description = "Non-traceable features of interest",
                        fnames = featureNames(tan2009r1)[111:113])
y
#> Object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   Non-traceable features of interest
#>  3 features of interest:
#>    Q9VT75, Q9VNA3, A8JNJ6

## an illegal FeaturesOfInterest
try(FeaturesOfInterest(description = "Won't work",
                       fnames = c("A", "Z", featureNames(tan2009r1)),
                       object = tan2009r1))
#> Error in FeaturesOfInterest(description = "Won't work", fnames = c("A",  : 
#>   2 feature(s) of interest absent from your object's feature names:
#>    A, Z.


FeaturesOfInterest(description = "This work, but not traceable",
                       fnames = c("A", "Z", featureNames(tan2009r1)))
#> Object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   This work, but not traceable
#>  890 features of interest:
#>    A, Z  ...  Q8SZM1, P07909



xx <- FoICollection()
xx
#> A collection of 0 features of interest.

xx <- addFeaturesOfInterest(x, xx)
xx <- addFeaturesOfInterest(y, xx)
names(xx) <- LETTERS[1:2]
xx
#> A collection of 2 features of interest.

## Sub-setting
xx[1]
#> A collection of 1 features of interest.
xx[[1]]
#> Traceable object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   A traceable test set of features of interest
#>  10 features of interest:
#>    P20353, P53501  ...  Q9VCK0, Q9VIU7
xx[["A"]]
#> Traceable object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   A traceable test set of features of interest
#>  10 features of interest:
#>    P20353, P53501  ...  Q9VCK0, Q9VIU7

description(xx)
#>                                              A 
#> "A traceable test set of features of interest" 
#>                                              B 
#>           "Non-traceable features of interest" 
foi(xx)
#> $A
#> Traceable object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   A traceable test set of features of interest
#>  10 features of interest:
#>    P20353, P53501  ...  Q9VCK0, Q9VIU7
#> 
#> $B
#> Object of class "FeaturesOfInterest"
#>  Created on Tue Oct 15 15:25:33 2024 
#>  Description:
#>   Non-traceable features of interest
#>  3 features of interest:
#>    Q9VT75, Q9VNA3, A8JNJ6
#> 

fnamesIn(x, tan2009r1)
#> [1] TRUE
fnamesIn(x, tan2009r1, count = TRUE)
#> [1] 10

rmFeaturesOfInterest(xx, 1)
#> A collection of 1 features of interest.