matchWCP {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


[Package Biostrings version 2.20.1 Index]