FindSets: Find all single linkage clusters in an undirected pairs list.

In npcooley/SynExtend: Tools for Working With Synteny Objects

Find all single linkage clusters in an undirected pairs list.

Description

Take in a pair of vectors representing the columns of an undirected pairs list and return the single linkage clusters.

Usage

FindSets(p1,
         p2,
         Verbose = FALSE)

Arguments

p1	Column 1 of a pairs matrix or list.
p2	Column 2 of a pairs matrix or list.
Verbose	Logical indicating whether or not to display a progress bar and print the time difference upon completion.

Details

FindSets uses a version of the union-find algorithm to collect single linkage clusters from a pairs list. Currently meant to be used inside a wrapper function, but left exposed for user convenience.

Value

A two column matrix with the first column being input nodes, and the second the node representing a single linkage cluster.

Author(s)

Nicholas Cooley [e-mail]

See Also

PairSummaries

Examples

set.seed(1986)
m <- cbind(as.integer(sample(30, size = 25,
                             replace = TRUE)),
           as.integer(sample(35, size = 25,
                             replace = TRUE)))

Levs <- unique(c(m[, 1],
                 m[, 2]))
m <- cbind("1" = as.integer(factor(x = m[, 1L],
                                   levels = Levs)),
           "2" = as.integer(factor(x = m[, 2L],
                                   levels = Levs)))
z <- FindSets(p1 = m[, 1],
              p2 = m[, 2])

npcooley/SynExtend documentation built on Nov. 15, 2024, 3:02 p.m.