matchWCP             package:Biostrings             R Documentation

A simple WCP matching function and related utilities

Description:

     A function implementing a simple algorithm for matching a set of
     patterns represented by Weighted Clustered Positions (WCP) to an
     XString sequence.

Usage:

       matchWCP(wcp, subject, min.score="80%")
       countWCP(wcp, subject, min.score="80%")
       WCPscoreStartingAt(wcp, subject, starting.at=1)

Arguments:

     wcp: A WCP object. 

 subject: An XString, XStringViews or MaskedXString object for
          'matchWCP' and 'countWCP'.

          A XString object for 'WCPscoreStartingAt'. 

min.score: The minimum score for counting a match. Can be given as a
          character string containing a percentage (e.g. '"85%"') of
          the highest possible score or as a single number. 

starting.at: An integer vector specifying the starting positions of the
          Weighted Clustered Positions relatively to the subject. 

Value:

     An XStringViews object for 'matchWCP'.

     A single integer for 'countWCP'.

     A numeric vector containing the Weighted Clustered Positions-based
     scores for 'WCPscoreStartingAt'.

Author(s):

     P. Aboyoun

See Also:

     'matchPWM', 'matchPattern', WCP-class, XString-class,
     XStringViews-class

