sDistMatrix is a distance matrix resulting from a call to
dist(seqs), where seqs is a
Sequences object. You may also just pass the
sequences and a call to dist will be done automatically.
clusterNumber
The number of clusters to create.
verbose
Controls how much logging information is printed.
type
There are two type options: "kmeans" and
"agglomerative". "kmeans" causes aclust to call
the normal kmeans method available in
R. "agglomerative" uses a hierarchical clustering technique on
the distance matrix.
knstart
The number of times to execute the "kmeans" algorithm to
ensure a global minimum is reached.
Value
aclust returns a list where each element represents a
cluster. Each element in the list is an array of integers, where each integer is the
index of sequence (the row of the input sequence matrix).
Details
During each round, the agglomerative clustering technique combines the points or sets of
points which have the smallest distance to one another. The distance
measure is the smallest pairwise distance between two sets of points.