peplib (version 1.5.1)

aclust: aclust

Description

Clusters a matrix of peptide sequences using kmeans or agglomerative clustering

Usage

aclust(sDistMatrix, clusterNumber, verbose = T, type = "kmeans", knstart
= 20)

Arguments

sDistMatrix

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.

See Also

Sequences, kmeans

Examples

#load some example data
data(TULASequences)

##Cluster
clusters <- aclust(dist(TULASequences), 3, knstart=1)
print(length(clusters[1]))
print(length(clusters[2]))
print(length(clusters[3]))