R: Calculates a Similarity Matrix for a Set of Fingerprints

fp.sim.matrix {fingerprint} | R Documentation

## 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` or `featvec` objects supplied 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

    fp.sim.matrix(fplist, fplist2=NULL, method='tanimoto')

### Arguments

`fplist` | A list structure with each element being an object of class `fingerprint` or `featvec`. These can be constructed by hand or read from disk via `fp.read`
`fplist2` | A list structure with each element being an object of class `fingerprint` or `featvec`. if `NULL` then traditional pairwise similarity is calculated with each member in `fplist`, otherwise the resultant N x M matrix is derived from the similarity between each member of `fplist` and `fplist2`
`method` | The type of distance metric to use. The default is `tanimoto`. Partial matching is supported.

### Value

A matrix with dimensions equal to `(length(fplist), length(fplist))` if `fplist2` is NULL, otherwise `(length(fplist), length(fplist2))`

### Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

### See Also

`distance`, `fp.read`

### Examples

    # 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) )

[Package fingerprint version 3.5.7 Index]