/fingerprint/man/bitspec.Rd

http://github.com/rajarshi/cdkr · Unknown · 46 lines · 44 code · 2 blank · 0 comment · 0 complexity · d839bab10da6f334946a447b19f4b559 MD5 · raw file

  1. \name{bit.spectrum}
  2. \alias{bit.spectrum}
  3. \title{
  4. Generate a Bit Spectrum from a List of Fingerprints
  5. }
  6. \description{
  7. The idea of comparing datasets using fingerprints was described in
  8. Guha \& Schurer (2008). The idea is that one can summarize the dataset
  9. by counting the frequency of occurrence of each bit position. The
  10. frequency is normalized by the number of fingerprints considered. Thus a
  11. collection of N fingerprints can be converted to a single vector of
  12. numbers highlighting the most frequent bits with respect to a given
  13. dataset. A plot of this vector looks like a traditional spectrum and
  14. hence the name.
  15. The bit spectra for two datasets (assuming that the same types of
  16. fingerprints have been used) allows one to compare the similarity of
  17. the datasets, without having to do a full pairwise similarity
  18. calculation. The difference between the structural features of the
  19. datasets can be quantified by evaluating the distance between the two
  20. bit spectra.
  21. }
  22. \usage{
  23. bit.spectrum(fplist)
  24. }
  25. \arguments{
  26. \item{fplist}{
  27. A list structure with each element being an object of class
  28. \code{fingerprint}. These will can be constructed by hand or
  29. read from disk via \code{\link{fp.read}}.
  30. All fingerprints in the list should be of the same length.
  31. }
  32. }
  33. \value{
  34. A numeric vector of length equal to the size of the fingerprints.
  35. }
  36. \seealso{
  37. \code{\link{distance}}, \code{\link{fp.read}}
  38. }
  39. \references{
  40. Guha, R.; Schurer, S.; \emph{J. Comp. Aid. Molec. Des.}, \bold{2008},
  41. \emph{22}, 367-384.
  42. }
  43. \keyword{programming}
  44. \author{Rajarshi Guha \email{rajarshi.guha@gmail.com}}