fp.sim.matrix {fingerprint}R Documentation

Calculates the similarity matrix for a set of fingerprints

Description

Given a set of fingerprints, a pairwise similarity can be calculated using the various distance metrics defined for binary strings. This function calculates the pairwise similarity matrix for a set of fingerprint vectors supplied in a list structure. Any of the distance metrics provided by fp.distance can be used and the default is the Tanimoto metric.

Note that if the the Euclidean distance is specified then the resultant matrix is a distance matrix and not a similarity matrix

Usage

fp.sim.matrix(fplist, size=1024, type='tanimoto')

Arguments

fplist A list structure with each element being a fingerprint vector. This structure will generally be obtained from fp.read.
size Length of the bit string represented by the fingerprint vector
type The type of distance metric to use. Alternatives are euclidean and dice and mt

Value

A matrix with dimensions equal to (length(fplist), length(fplist))

Author(s)

Rajarshi Guha rguha@indiana.edu

See Also

fp.distance, fp.read

Examples

# make a fingerprint vector
fp1 <- fp.from.bstring("110011")
fp2 <- fp.from.bstring("100111")
fp3 <- fp.from.bstring("011111")

fp.sim.matrix( list(fp1,fp2,fp3), size=6)

[Package fingerprint version 1.6 Index]