matchLRPatterns {Biostrings} | R Documentation |
matchLRPatterns(Lpattern, Rpattern, max.ngaps, subject, Lmismatch=0, Rmismatch=0, Lfixed=TRUE, Rfixed=TRUE)
Lpattern |
The left part of the pattern. |
Rpattern |
The right part of the pattern. |
max.ngaps |
The max number of gaps in the middle i.e the max distance between the left and right parts of the pattern. |
subject |
A BString (or derived) object containing the target sequence. |
Lmismatch |
The number of mismatches allowed for the left part of the pattern.
If non-zero, a fuzzy string searching algorithm is used for matching
(see the matchPattern function for more information).
|
Rmismatch |
Same as Lmismatch but for the right part of the pattern.
|
Lfixed |
Only with a DNAString or RNAString subject can a Lfixed
value other than the default (TRUE ) be used.
With Lfixed=FALSE , ambiguities (i.e. letters from the IUPAC Extended
Genetic Alphabet (see IUPAC_CODE_MAP ) that are not from the
base alphabet) in the left pattern _and_ in the subject are interpreted as
wildcards i.e. they match any letter that they stand for.
See the fixed argument of the matchPattern function
for more information.
|
Rfixed |
Same as Lfixed but for the right part of the pattern.
|
A BStringViews object containing all the matches, even when they are overlapping (see the examples below), and where the matches are ordered from left to right (i.e. by ascending starting position).
H. Pages
matchPattern
,
matchProbePair
,
findPalindromes
,
reverseComplement
,
BStringViews
library(BSgenome.Dmelanogaster.FlyBase.r51) subject <- Dmelanogaster[["3R"]] Lpattern <- "AGCTCCGAG" Rpattern <- "TTGTTCACA" matchLRPatterns(Lpattern, Rpattern, 500, subject) # 1 match ## Note that matchLRPatterns() will return all matches, even when they are ## overlapping: subject <- DNAString("AAATTAACCCTT") matchLRPatterns("AA", "TT", 0, subject) # 1 match matchLRPatterns("AA", "TT", 1, subject) # 2 matches matchLRPatterns("AA", "TT", 3, subject) # 3 matches matchLRPatterns("AA", "TT", 7, subject) # 4 matches