Calculates a 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 objectssupplied in a list structure. Any of the distance metrics provided by 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

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fp.sim.matrix(fplist, method='tanimoto')

Arguments

fplist

A list structure with each element being an object of class fingerprint. These will can be constructed by hand or read from disk via fp.read

method

The type of distance metric to use. Alternatives are euclidean and dice and mt. The default is tanimoto. Partial matching is supported.

Value

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

Author(s)

Rajarshi Guha rguha@indiana.edu

See Also

distance, fp.read

Examples

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# make fingerprint objects
fp1 <- new("fingerprint", nbit=6, bits=c(1,2,5,6))
fp2 <- new("fingerprint", nbit=6, bits=c(1,4,5,6))
fp3 <- new("fingerprint", nbit=6, bits=c(2,3,4,5,6))

fp.sim.matrix( list(fp1,fp2,fp3) )