FeatureSetCollection {ClassifyR} | R Documentation

## 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

A method which summarises the results is available. `featureSets` is a `FeatureSetCollection` object.

  `show(featureSets)`Prints a short summary of what `featureSets` contains.

### Subsetting

The FeatureSetCollection may be subsetted 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

[Package ClassifyR version 2.4.4 Index]