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

### See Also

dist, agrep, pairwiseAlignment, substitution.matrices

### 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 2.62.0 Index]