matchPattern {Biostrings}R Documentation

String searching functions

Description

Generic that finds all matches of a pattern in a BString. Currently only the ``shift-or'' algorithm is available.

Usage

  matchPattern(pattern, subject, algorithm="shift-or", mismatch=0, fixed=NA)
  countPattern(pattern, subject, algorithm="shift-or", mismatch=0, fixed=NA)
  mismatch(pattern, x, fixed=NA)

Arguments

pattern The pattern string.
subject A BString (or DNAString or RNAString) object containing the subject string.
algorithm One of the following: "boyer-moore", "forward-search" or "shift-or" (currently, only "shift-or" is available).
mismatch The number of mismatches allowed. If non-zero a fuzzy string searching algorithm is used for matching.
fixed A logical. If TRUE, pattern is a string to be matched as is.
x A BStringViews object (typically, one returned by code{matchPattern(pattern, subject)}).

Details

Value

Author(s)

H. Pages

See Also

Examples






[Package Biostrings version 2.0.3 Index]