FeatureSetCollection: Container for Storing A Collection of Sets

In DarioS/ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Container for Storing A Collection of Sets

Description

This container is the required storage format for a collection of sets. Typically, the elements of a set will either be a set of proteins (i.e. character vector) which perform a particular biological process or a set of binary interactions (i.e. Two-column matrix of feature identifiers).

Constructor

FeatureSetCollection(sets)

sets

A named list. The names of the list describe the sets and the elements of the list specify the features which comprise the sets.

Summary

featureSets is a FeatureSetCollection object.

show(featureSets): Prints a short summary of what featureSets contains.
length(featureSets): Prints how many sets of features there are.

Subsetting

The FeatureSetCollection may be subsetted to a smaller set of elements or a single set may be extracted as a vector.

featureSets is a FeatureSetCollection object.

featureSets[i:j]: Reduces the object to a subset of the feature sets between elements i and j of the collection.
featureSets[[i]]: Extract the feature set identified by i. i may be a numeric index or the character name of a feature set.

Author(s)

Dario Strbenac

Examples

    ontology <- list(c("SESN1", "PRDX1", "PRDX2", "PRDX3", "PRDX4", "PRDX5", "PRDX6",
                       "LRRK2", "PARK7"),
                     c("ATP7A", "CCS", "NQO1", "PARK7", "SOD1", "SOD2", "SOD3",
                       "SZT2", "TNF"),
                     c("AARS", "AIMP2", "CARS", "GARS", "KARS", "NARS", "NARS2",
                       "LARS2", "NARS", "NARS2", "RGN", "UBA7"),
                     c("CRY1", "CRY2", "ONP1SW", "OPN4", "RGR"),
                     c("ESRRG", "RARA", "RARB", "RARG", "RXRA", "RXRB", "RXRG"),
                     c("CD36", "CD47", "F2", "SDC4"),
                     c("BUD31", "PARK7", "RWDD1", "TAF1")
                     )
    names(ontology) <- c("Peroxiredoxin Activity", "Superoxide Dismutase Activity",
                         "Ligase Activity", "Photoreceptor Activity",
                         "Retinoic Acid Receptor Activity",
                         "Thrombospondin Receptor Activity",
                         "Regulation of Androgen Receptor Activity")
                         
    featureSets <- FeatureSetCollection(ontology)
    featureSets
    featureSets[3:5]
    featureSets[["Photoreceptor Activity"]]
    
    subNetworks <- list(MAPK = matrix(c("NRAS", "NRAS", "NRAS", "BRAF", "MEK",
                                        "ARAF", "BRAF", "CRAF", "MEK", "ERK"), ncol = 2),
                        P53 = matrix(c("ATM", "ATR", "ATR", "P53",
                                       "CHK2", "CHK1", "P53", "MDM2"), ncol = 2)
                        )
    networkSets <- FeatureSetCollection(subNetworks)                        
    networkSets
    

DarioS/ClassifyR documentation built on Nov. 4, 2024, 1:06 p.m.