XNAPairwiseAlignment {XNAString}R Documentation

Pairwise alignment methods for XNAString object

Description

This function performs pairwise alignment for sequences stored in target slot of XNAString object with subject

Usage

XNAPairwiseAlignment(pattern, subject, ...)

## S4 method for signature 'XNAString,character'
XNAPairwiseAlignment(
  pattern,
  subject,
  type = "global",
  substitutionMatrix = NULL,
  fuzzyMatrix = NULL,
  gapOpening = 10,
  gapExtension = 4,
  scoreOnly = FALSE
)

Arguments

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.

Value

an instance of class PairwiseAlignments

Examples

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
  )

[Package XNAString version 1.2.0 Index]