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"`, `"hamming"`, `"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 upper triangle of the matrix should be printed by `print.dist`.
`type`	(applicable when `method = "quality"` or `method = "substitutionMatrix"`). 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.
`quality`	(applicable when `method = "quality"`). object of class `XStringQuality` representing the quality scores for `x` that are used in a quality-based method for generating a substitution matrix.
`substitutionMatrix`	(applicable when `method = "substitutionMatrix"`). symmetric matrix representing the fixed substitution scores in the alignment.
`fuzzyMatrix`	(applicable when `method = "quality"`). 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`	(applicable when `method = "quality"` or `method = "substitutionMatrix"`). penalty for opening a gap in the alignment.
`gapExtension`	(applicable when `method = "quality"` or `method = "substitutionMatrix"`). penalty for extending a gap in the alignment
`...`	optional arguments to generic function to support additional methods.

Details

When method = "hamming", uses the underlying neditStartingAt code to calculate the distances, where the Hamming distance is defined as the number of substitutions between two strings of equal length. Otherwise, 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 2.46.0 Index]