trimLRPatterns {Biostrings} | R Documentation |
The trimLRPatterns
function trims left and/or right flanking patterns
from sequences.
trimLRPatterns(Lpattern = "", Rpattern = "", subject, max.Lmismatch = 0, max.Rmismatch = 0, with.Lindels = FALSE, with.Rindels = FALSE, Lfixed = TRUE, Rfixed = TRUE, ranges = FALSE)
Lpattern |
The left pattern. |
Rpattern |
The right pattern. |
subject |
An XString object, XStringSet object, or character vector containing the target sequence(s). |
max.Lmismatch |
Either an integer vector of length nLp = nchar(Lpattern)
representing an absolute number of mismatches (or edit distance if
with.Lindels is TRUE ) or a single numeric value in the
interval [0, 1) representing a mismatch rate when aligning
terminal substrings (suffixes) of Lpattern with the beginning
(prefix) of subject following the conventions set by
neditStartingAt , isMatchingStartingAt ,
etc.
When
Otherwise,
Once the integer vector is constructed using the rules given above, when
For a given element |
max.Rmismatch |
Same as max.Lmismatch but with Rpattern , along with
with.Rindels (below), and its initial segments (prefixes)
substring(Rpattern, 1, i) .
For a given element |
with.Lindels |
If TRUE , indels are allowed in the alignments of the suffixes
of Lpattern with the subject, at its beginning.
See the with.indels arguments of the matchPattern
and neditStartingAt functions for detailed information.
|
with.Rindels |
Same as with.Lindels but for alignments of the prefixes of
Rpattern with the subject, at its end.
See the with.indels arguments of the matchPattern
and neditEndingAt functions for detailed information.
|
Lfixed, Rfixed |
Whether IUPAC extended letters in the left or right pattern should
be interpreted as ambiguities (see ?`lowlevel-matching`
for the details).
|
ranges |
If TRUE , then return the ranges to use to trim subject .
If FALSE , then returned the trimmed subject .
|
A new XString object, XStringSet object, or character vector with the "longest" flanking matches removed, as described above.
P. Aboyoun and H. Jaffee
matchPattern
,
matchLRPatterns
,
lowlevel-matching,
XString-class,
XStringSet-class
Lpattern <- "TTCTGCTTG" Rpattern <- "GATCGGAAG" subject <- DNAString("TTCTGCTTGACGTGATCGGA") subjectSet <- DNAStringSet(c("TGCTTGACGGCAGATCGG", "TTCTGCTTGGATCGGAAG")) ## Only allow for perfect matches on the flanks trimLRPatterns(Lpattern = Lpattern, subject = subject) trimLRPatterns(Rpattern = Rpattern, subject = subject) trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet) ## Allow for perfect matches on the flanking overlaps trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet, max.Lmismatch = 0, max.Rmismatch = 0) ## Allow for mismatches on the flanks trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subject, max.Lmismatch = 0.2, max.Rmismatch = 0.2) maxMismatches <- as.integer(0.2 * 1:9) maxMismatches trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet, max.Lmismatch = maxMismatches, max.Rmismatch = maxMismatches) ## Produce ranges that can be an input into other functions trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet, max.Lmismatch = 0, max.Rmismatch = 0, ranges = TRUE) trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subject, max.Lmismatch = 0.2, max.Rmismatch = 0.2, ranges = TRUE)