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/fingerprint/man/sim.Rd

http://github.com/rajarshi/cdkr
Unknown | 52 lines | 50 code | 2 blank | 0 comment | 0 complexity | a0c7e4abd4c8f6c862240cc08764cd50 MD5 | raw file
 1\name{fp.sim.matrix}
 2\alias{fp.sim.matrix}
 3\title{
 4  Calculates a Similarity Matrix for a Set of Fingerprints
 5}
 6\description{
 7Given a set of fingerprints, a pairwise similarity can be calculated using the
 8various distance metrics defined for binary strings. This function calculates
 9the pairwise similarity matrix for a set of \code{fingerprint} or
10\code{featvec} objects supplied in a \code{list} 
11structure. Any of the distance metrics provided by \code{\link{distance}} can be used and the 
12default is the Tanimoto metric.
13
14Note that if the the Euclidean distance is specified then the resultant matrix is a
15distance matrix and not a similarity matrix
16}
17\usage{
18fp.sim.matrix(fplist, fplist2=NULL, method='tanimoto')
19}
20\arguments{
21  \item{fplist}{
22        A list structure with each element being an object of class
23	\code{fingerprint} or \code{featvec}. These can be constructed by hand or
24	read from disk via \code{\link{fp.read}}    
25    }
26\item{fplist2}{A list structure with each element being an object of class
27\code{fingerprint} or \code{featvec}. if \code{NULL} then traditional pairwise 
28similarity is calculated with each member in \code{fplist}, otherwise the 
29resultant N x M matrix is derived from the similarity between each member of 
30\code{fplist} and \code{fplist2}}
31    \item{method}{
32    The type of distance metric to use. The default is \code{tanimoto}. Partial
33    matching is supported.
34    }
35}
36\value{
37A matrix with dimensions equal to \code{(length(fplist), length(fplist))} if 
38\code{fplist2} is NULL, otherwise \code{(length(fplist), length(fplist2))}
39}
40\seealso{
41    \code{\link{distance}}, \code{\link{fp.read}}
42}
43\examples{
44# make fingerprint objects
45fp1 <- new("fingerprint", nbit=6, bits=c(1,2,5,6))
46fp2 <- new("fingerprint", nbit=6, bits=c(1,4,5,6))
47fp3 <- new("fingerprint", nbit=6, bits=c(2,3,4,5,6))
48
49fp.sim.matrix( list(fp1,fp2,fp3) )
50}
51\keyword{logic}
52\author{Rajarshi Guha \email{rajarshi.guha@gmail.com}}