/fingerprint/man/bitspec.Rd
http://github.com/rajarshi/cdkr · Unknown · 46 lines · 44 code · 2 blank · 0 comment · 0 complexity · d839bab10da6f334946a447b19f4b559 MD5 · raw file
- \name{bit.spectrum}
- \alias{bit.spectrum}
- \title{
- Generate a Bit Spectrum from a List of Fingerprints
- }
- \description{
- The idea of comparing datasets using fingerprints was described in
- Guha \& Schurer (2008). The idea is that one can summarize the dataset
- by counting the frequency of occurrence of each bit position. The
- frequency is normalized by the number of fingerprints considered. Thus a
- collection of N fingerprints can be converted to a single vector of
- numbers highlighting the most frequent bits with respect to a given
- dataset. A plot of this vector looks like a traditional spectrum and
- hence the name.
- The bit spectra for two datasets (assuming that the same types of
- fingerprints have been used) allows one to compare the similarity of
- the datasets, without having to do a full pairwise similarity
- calculation. The difference between the structural features of the
- datasets can be quantified by evaluating the distance between the two
- bit spectra.
- }
- \usage{
- bit.spectrum(fplist)
- }
- \arguments{
- \item{fplist}{
- A list structure with each element being an object of class
- \code{fingerprint}. These will can be constructed by hand or
- read from disk via \code{\link{fp.read}}.
- All fingerprints in the list should be of the same length.
- }
- }
- \value{
- A numeric vector of length equal to the size of the fingerprints.
- }
- \seealso{
- \code{\link{distance}}, \code{\link{fp.read}}
- }
- \references{
- Guha, R.; Schurer, S.; \emph{J. Comp. Aid. Molec. Des.}, \bold{2008},
- \emph{22}, 367-384.
- }
- \keyword{programming}
- \author{Rajarshi Guha \email{rajarshi.guha@gmail.com}}