R: String Distance/Alignment Score Matrix

stringDist {Biostrings}

R Documentation

String Distance/Alignment Score Matrix

Description

Computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Usage

stringDist(x, method = "levenshtein", ignoreCase = FALSE, diag = FALSE, upper = FALSE, ...)
## S4 method for signature 'XStringSet':
stringDist(x, method = "levenshtein", ignoreCase = FALSE, diag = FALSE,
                   upper = FALSE, type = "global", quality = PhredQuality(22L),
                   substitutionMatrix = NULL, fuzzyMatrix = NULL, gapOpening = 0,
                   gapExtension = -1)
## S4 method for signature 'QualityScaledXStringSet':
stringDist(x, method = "quality", ignoreCase = FALSE,
                   diag = FALSE, upper = FALSE, type = "global", substitutionMatrix = NULL,
                   fuzzyMatrix = NULL, gapOpening = 0, gapExtension = -1)

Arguments

`x`	a character vector or an `XStringSet` object.
`method`	calculation method. One of `"levenshtein"`, `"quality"`, or `"substitutionMatrix"`.
`ignoreCase`	logical value indicating whether to ignore case during scoring.
`diag`	logical value indicating whether the diagonal of the matrix should be printed by `print.dist`.
`upper`	logical value indicating whether the diagonal of the matrix should be printed by `print.dist`.
`type`	type of alignment. One of `"global"`, `"local"`, and `"overlap"`, where `"global"` = align whole strings with end gap penalties, `"local"` = align string fragments, `"overlap"` = align whole strings without end gap penalties. This argument is ignored if `method == "levenshtein"`.
`quality`	object of class `XStringQuality` representing the quality scores for `x` that are used in a quality-based method for generating a substitution matrix. This argument is ignored if `method != "quality"`.
`substitutionMatrix`	symmetric substitution matrix for a non-quality based alignment. This argument is ignored if `method != "substitutionMatrix"`.
`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`	penalty for opening a gap in the alignment. This argument is ignored if `method == "levenshtein"`.
`gapExtension`	penalty for extending a gap in the alignment. This argument is ignored if `method == "levenshtein"`.
`...`	optional arguments to generic function to support additional methods.

Details

Uses the underlying pairwiseAlignment code to compute the distance/alignment score matrix.

Value

Returns an object of class "dist".

Author(s)

P. Aboyoun

Examples

  stringDist(c("lazy", "HaZy", "crAzY"))
  stringDist(c("lazy", "HaZy", "crAzY"), ignoreCase = TRUE)

  data(phiX174Phage)
  plot(hclust(stringDist(phiX174Phage), method = "single"))

  data(srPhiX174)
  stringDist(srPhiX174[1:4])
  stringDist(srPhiX174[1:4], method = "quality",
             quality = SolexaQuality(quPhiX174[1:4]),
             gapOpening = -10, gapExtension = -4)

[Package Biostrings version 2.10.22 Index]