distGraph-class: Class "distGraph"

In pshannon-bioc/graph: graph: A package to handle graph data structures

Description

A class definition for graphs that are based on distances.

Objects from the Class

Objects can be created by calls of the form new("distGraph", ...).

Slots

Dist:

Object of class "dist" that forms the basis for the edge weights used in the distGraph.

Extends

Class "graph", directly.

Methods

show

signature(object = "distGraph"): a print method

Dist

signature(object = "distGraph"): return the dist object.

adj

signature(object = "distGraph"): find the nodes adjacent to the supplied node.

nodes

signature(object = "distGraph"): return the nodes in the graph.

numNodes

signature(object = "distGraph"): return the number of nodes.

threshold

signature(object = "distGraph", k, value): set all distances that are larger than the supplied threshold, k, to the supplied value. The default is value is zero (and so is appropriate for similarities, rather than distances).

initialize

signature(object = "distGraph"): initialize a distGraph instance.

edgeWeights

Return a list of edge weights in a list format similar to the edges method.

edgeL

signature(graph = "distGraph"): A method for obtaining the edge list.

Author(s)

R. Gentleman

References

Shamir's paper and Butte et al

See Also

graph-class, clusterGraph-class

Examples

   set.seed(123)
   x <- rnorm(26)
   names(x) <- letters
   library(stats)
   d1 <- dist(x)
   g1 <- new("distGraph", Dist=d1)

pshannon-bioc/graph documentation built on May 26, 2019, 10:32 a.m.