stringDist {Biostrings} | R Documentation |
Computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.
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)
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. |
Uses the underlying pairwiseAlignment code to compute the distance/alignment score matrix.
Returns an object of class "dist"
.
P. Aboyoun
dist, agrep, pairwiseAlignment, substitution.matrices
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)