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" ,
"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. |
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.
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)