matchPattern {Biostrings} | R Documentation |
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.
matchPattern(pattern, subject, algorithm="auto", mismatch=0, fixed=TRUE) countPattern(pattern, subject, algorithm="auto", mismatch=0, fixed=TRUE) mismatch(pattern, x, fixed=TRUE)
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)}). |
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