stringDist            package:Biostrings            R Documentation

_S_t_r_i_n_g _D_i_s_t_a_n_c_e/_A_l_i_g_n_m_e_n_t _S_c_o_r_e _M_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     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)

_A_r_g_u_m_e_n_t_s:

       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: (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.

_D_e_t_a_i_l_s:

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

_V_a_l_u_e:

     Returns an object of class '"dist"'.

_A_u_t_h_o_r(_s):

     P. Aboyoun

_S_e_e _A_l_s_o:

     dist, agrep, pairwiseAlignment, substitution.matrices

_E_x_a_m_p_l_e_s:

       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)

