XNAMatchPDict {XNAString} | R Documentation |
This is function finding all the occurrences of a given set of patterns (typically short) in a (typically long) reference sequence
XNAMatchPDict( pdict, subject, max.mismatch = 0, min.mismatch = 0, with.indels = FALSE, fixed = TRUE, algorithm = "auto", verbose = FALSE ) ## S4 method for signature 'XNAString,character' XNAMatchPDict( pdict, subject, max.mismatch = 0, min.mismatch = 0, with.indels = FALSE, fixed = TRUE, algorithm = "auto", verbose = FALSE ) ## S4 method for signature 'XNAString,XString' XNAMatchPDict( pdict, subject, max.mismatch = 0, min.mismatch = 0, with.indels = FALSE, fixed = TRUE, algorithm = "auto", verbose = FALSE )
pdict |
XNAString object, target slot taken as pdict object from Biostrings |
subject |
string containing sequence |
max.mismatch |
The maximum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used. |
min.mismatch |
The minimum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used. |
with.indels |
If TRUE then indels are allowed. In that case, min.mismatch must be 0 and max.mismatch is interpreted as the maximum "edit distance" allowed between the pattern and a match. Note that in order to avoid pollution by redundant matches, only the "best local matches" are returned. Roughly speaking, a "best local match" is a match that is locally both the closest (to the pattern P) and the shortest. |
fixed |
If TRUE (the default), an IUPAC ambiguity code in the pattern can only match the same code in the subject, and vice versa. If FALSE, an IUPAC ambiguity code in the pattern can match any letter in the subject that is associated with the code, and vice versa. |
algorithm |
One of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", "shift-or" or "indels". |
verbose |
TRUE or FALSE. |
an MIndex object of length M
, and countPDict
an integer vector of length M
.
s2 <- XNAString::XNAString( base = "GCGGAGAGAGCACAGATACA", sugar = "FODDDDDDDDDDDDDDDDDD", target = Biostrings::DNAStringSet(c( "GGCGGAGAGAGCACAGATACA", "GGCGGAGAGAGCACAGATACA" )) ) o <- XNAString::XNAMatchPDict( s2, "GGCGGAGAGAGCACAGATACAGGGGCGGAGAGAGCACAGATACACGGAGAGAGCACAGATACA" )