PairwiseAlignedFixedSubject-class package:Biostrings R Documentation

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

     The 'PairwiseAlignedFixedSubject' class is a container for storing
     an alignment. The 'PairwiseAlignedFixedSubjectSummary' class is a
     container for storing the summary of an alignment.

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

     Before we define the notion of alignment, we introduce the notion
     of "filled-with-gaps subsequence". A "filled-with-gaps
     subsequence" of a string string1 is obtained by inserting 0 or any
     number of gaps in a subsequence of s1. For example L-A-ND and
     A-N-D are "filled-with-gaps subsequences" of LAND. An alignment
     between two strings string1 and string2 results in two strings
     (align1 and align2) that have the same length and are
     "filled-with-gaps subsequences" of string1 and string2.

     For example, this is an alignment between LAND and LEAVES:


         L-A
         LEA

     An alignment can be seen as a compact representation of one set of
     basic operations that transforms string1 into align1. There are 3
     different kinds of basic operations: "insertions" (gaps in
     align1), "deletions" (gaps in align2),  "replacements". The above
     alignment represents the following basic operations:


         insert E at pos 2
         insert V at pos 4
         insert E at pos 5
         replace by S at pos 6 (N is replaced by S)
         delete at pos 7 (D is deleted)

     Note that "insert X at pos i" means that all letters at a position
     >= i are moved 1 place to the right before X is actually inserted.

     There are many possible alignments between two given strings
     string1 and string2 and a common problem is to find the one (or
     those ones) with the highest score, i.e. with the lower total cost
     in terms of basic operations.

_A_c_c_e_s_o_r _m_e_t_h_o_d_s:

     In the code snippets below, 'x' is a 'PairwiseAlignedFixedSubject'
     object, except otherwise noted.


      'pattern(x)': The 'AlignedXStringSet' object for the pattern.

      'subject(x)': The 'AlignedXStringSet' object for the subject.

      'type(x)': The type of the alignment ('"global"', '"local"',
          '"overlap"', '"patternOverlap"', or '"subjectOverlap"').
          There is a method for 'PairwiseAlignedFixedSubjectSummary' as
          well.

      'score(x)': The score of the alignment (integer). There is a
          method for 'PairwiseAlignedFixedSubjectSummary' as well.

      'nindel(x)': An 'InDel' object containing the number of
          insertions and deletions.

      'length(x)': The length of the 'aligned(pattern(x))' and
          'aligned(subject(x))'. There is a method for
          'PairwiseAlignedFixedSubjectSummary' as well.

      'nchar(x)': The nchar of the 'aligned(pattern(x))' and
          'aligned(subject(x))'. There is a method for
          'PairwiseAlignedFixedSubjectSummary' as well.

      'alphabet(x)': Equivalent to 'alphabet(unaligned(subject(x)))'.

      'summary(object, ...)': Generates a summary for the
          'PairwiseAlignedFixedSubject'.

      'aligned(x)': Returns an 'XStringSet' object containing the
          aligned patterns without insertions. This operation ``aligns"
          the alignments.

      'as.character(x)': Converts 'aligned(x)' to a character vector.

      'as.matrix(x)': Returns an "exploded" character matrix
          representation of 'aligned(x)'.

      'Views(subject, start=NA, end=NA, names=NULL)': The
          'XStringViews' object that represents the pairwise alignments
          along 'unaligned(subject(subject))'. The 'start' and 'end'
          arguments must be either 'NA' or an integer vector of length
          1 that denotes the offset from 'start(subject(subject))'.

      'toString(x)': Equivalent to 'toString(as.character(x))'.


_S_u_b_s_e_t_t_i_n_g _m_e_t_h_o_d_s:


      'x[i]': Returns a new 'PairwiseAlignedFixedSubject' object made
          of the selected elements.

      'rep(x, times)': Returns a new 'PairwiseAlignedFixedSubject'
          object made of the repeated elements.


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

     P. Aboyoun and H. Pages

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

     'pairwiseAlignment', 'AlignedXStringSet-class', 'XString-class',
     'XStringViews-class', 'match-utils'

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

       pattern <- AAStringSet(c("HLDNLKGTF", "HVDDMPNAL"))
       subject <- AAString("SMDDTEKMSMKL")
       nw1 <- pairwiseAlignment(pattern, subject, substitutionMatrix = "BLOSUM50", gapOpening = -3, gapExtension = -1)
       pattern(nw1)
       subject(nw1)
       aligned(nw1)
       as.character(nw1)
       as.matrix(nw1)
       nchar(nw1)
       score(nw1)
       nw1

