| XNAPairwiseAlignment {XNAString} | R Documentation |
This function performs pairwise alignment for sequences stored in target slot of XNAString object with subject
XNAPairwiseAlignment(pattern, subject, ...) ## S4 method for signature 'XNAString,character' XNAPairwiseAlignment( pattern, subject, type = "global", substitutionMatrix = NULL, fuzzyMatrix = NULL, gapOpening = 10, gapExtension = 4, scoreOnly = FALSE )
pattern |
XNAString object, pattern taken from target slot. |
subject |
a character vector of length 1, an XString, or an XStringSet object of length 1. |
... |
optional arguments to generic function to support additional methods |
type |
type of alignment. One of "global", "local", "overlap", "global-local", and "local-global" where "global" = align whole strings with end gap penalties, "local" = align string fragments, "overlap" = align whole strings without end gap penalties, "global-local" = align whole strings in pattern with consecutive subsequence of subject, "local-global" = align consecutive subsequence of pattern with whole strings in subject. |
substitutionMatrix |
substitution matrix representing the fixed substitution scores for an alignment. It cannot be used in conjunction with patternQuality and subjectQuality arguments. |
fuzzyMatrix |
fuzzy match matrix for quality-based alignments. It takes values between 0 and 1; where 0 is an unambiguous mismatch, 1 is an unambiguous match, and values in between represent a fraction of "matchiness". |
gapOpening |
the cost for opening a gap in the alignment. |
gapExtension |
the incremental cost incurred along the length of the gap in the alignment. |
scoreOnly |
logical to denote whether or not to return just the scores of the optimal pairwise alignment. |
an instance of class PairwiseAlignments
mat <-
Biostrings::nucleotideSubstitutionMatrix(
match = 1,
mismatch = -3,
baseOnly = TRUE
)
s1 <-
XNAString::XNAString(
base = "GCGGAGAGAGCACAGATACA",
sugar = "FODDDDDDDDDDDDDDDDDD",
target = Biostrings::DNAStringSet("GGCGGAGAGAGCACAGATACA")
)
XNAString::XNAPairwiseAlignment(s1,
"ACCCACACACACACACACACAC",
"global",
substitutionMatrix = mat
)