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 1.2.2 Index]