RangesMatching-class         package:IRanges         R Documentation

_M_a_t_c_h_i_n_g_s _b_e_t_w_e_e_n _R_a_n_g_e_s

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

     The 'RangesMatching' class stores a set of matchings between the
     ranges in one 'Ranges' instance and the ranges in another.
     Currently, 'RangesMatching' are used to represent the result of an
     'overlap' query, though other matching operations are imaginable.

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

     The matchings between the ranges are stored as a 'Matrix-class'
     instance. While that structure is accessible, it is usually more
     convenient to coerce the 'RangesMatching' instance to a more
     amenable representation.

     The 'as.matrix' method coerces a 'RangesMatching' to a two column
     'matrix' with one row for each matching, where the value in the
     first column is the index of a range in the first (query) 'Ranges'
     and the index of the matched subject range is in the second
     column.

     The 'as.table' method counts the number of matchings for each
     query range and outputs the counts as a 'table'.

     To transpose a 'RangesMatrix' 'x', so that the subject and query
     are interchanged, call 't(x)'. This allows, for example, counting
     the number of subjects that matched using 'as.table'.

_C_o_e_r_c_i_o_n:

     In the code snippets below, 'x' is a 'RangesMatching' object.


      'as.matrix(x)': Coerces 'x' to a two column integer matrix, with
          each row representing a matching between a query index (first
          column) and subject index (second column).

      'as.table(x)': counts the number of matchings for each query
          range in 'x' and outputs the counts as a 'table'.

      't(x)': Interchange the query and subject in 'x', returns a
          transposed 'RangesMatching'.

_A_c_c_e_s_s_o_r_s:


      'matchMatrix(x)': Get the 'Matrix-class', which may be a dense
          logical matrix ('lgeMatrix-class') or sparse non-zero pattern
          matrix ('ngCMatrix-class'), that encodes the matchings, with
          columns corresponding to query ranges and rows corresponding
          to subject ranges. It is not recommended to work with this
          matrix directly, unless the coercion methods above are
          inadequate.


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

     Michael Lawrence

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

     'overlap', which generates an instance of this class.

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

       query <- IRanges(c(1, 4, 9), c(5, 7, 10))
       subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
       tree <- IntervalTree(subject)
       matchings <- overlap(tree, query)

       as.matrix(matchings)

       if (interactive()) {
         ## This code seems to not work anymore (because of a change in
         ## the Matrix package?)
         as.table(matchings) # hits per query
         as.table(t(matchings)) # hits per subject
       }

