FeatureSetCollection {ClassifyR} | R Documentation |
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).
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.
A method which summarises the results is available.
featureSets
is a FeatureSetCollection
object.
show(featureSets)
Prints a short summary of what featureSets
contains.
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.
Dario Strbenac
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