matchPattern {Biostrings}R Documentation

String searching functions

Description

Generic that finds all matches of a pattern in a BString. Currently only a ``Boyer-Moore-like'' algorithm and the ``shift-or'' algorithm are available.

Usage

  matchPattern(pattern, subject, algorithm="auto", mismatch=0, fixed=TRUE)
  countPattern(pattern, subject, algorithm="auto", mismatch=0, fixed=TRUE)
  mismatch(pattern, x, fixed=TRUE)

Arguments

pattern The pattern string.
subject A BString (or DNAString or RNAString) object containing the subject string.
algorithm One of the following: "auto", "naive", "boyer-moore", "forward-search" or "shift-or" (note that "forward-search" is not available yet).
mismatch The number of mismatches allowed. If non-zero a fuzzy string searching algorithm is used for matching.
fixed A logical. Only DNAString or RNAString support fixed=FALSE. In this case, ambiguities (i.e. letters from the IUPAC Extended Genetic Alphabet (see IUPAC_CODE_MAP) that are not from the base alphabet) match any letter that they stand for.
x A BStringViews object (typically, one returned by code{matchPattern(pattern, subject)}).

Details

Value

Author(s)

H. Pages

See Also

Examples






[Package Biostrings version 2.4.8 Index]