fp.sim.matrix {fingerprint} | R Documentation |
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
fp.sim.matrix(fplist, size=1024, type='tanimoto')
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
|
A matrix with dimensions equal to (length(fplist), length(fplist))
Rajarshi Guha rguha@indiana.edu
# 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)