RangesMatchingList-class       package:IRanges       R Documentation

List of Matchings between Ranges

Description:

     The 'RangesMatchingList' class stores a set of matchings,
     represented as 'RangesMatching' objects, between the ranges in one
     'RangesList' object and the ranges in another.

Details:

     Roughly the same set of utilities are provided for
     'RangesMatchingList' as for 'RangesMatching':

     The 'as.matrix' method coerces a 'RangesMatchingList' in a similar
     way to 'RangesMatching', except a column is prepended that
     indicates which space (or element in the query 'RangesList') to
     which the row corresponds.

     The 'as.table' method flattens or unlists the list, counts the
     number of matchings for each query range and outputs the counts as
     a 'table', which has the same shape as from a single
     'RangesMathing'.

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

     To get the actual regions of intersection between the overlapping
     ranges, use the 'ranges' accessor.

Coercion:

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


      'as.matrix(x)': calls 'as.matrix' on each 'RangesMatching',
          combines them row-wise and offsets the indices so that they
          are aligned with the result of calling 'unlist' on the query
          and subject.

      'as.table(x)': counts the number of matchings for each query
          range in 'x' and outputs the counts as a 'table', which is
          aligned with the result of calling 'unlist' on the query.

      't(x)': Interchange the query and subject in each space of 'x',
          returns a transposed 'RangesMatchingList'.

Accessors:


      'queryHits(x)': Gets the indices of overlapping ranges in the
          query, equivalent to 'as.matrix(x)[,1]'.

      'subjectHits(x)': Gets the indices of overlapping ranges in the
          subject, equivalent to 'as.matrix(x)[,2]'.

      'space(x)': gets the character vector naming the space in the
          query 'RangesList' for each match, or 'NULL' if the query did
          not have any names.

      'ranges(x, query, subject)': returns a 'RangesList' holding the
          intersection of the ranges in the 'RangesList' objects
          'query' and 'subject', which should be the same subject and
          query used to generate 'x'. Eventually, we might store the
          query and subject inside 'x', in which case the arguments
          would be redundant.


Note:

     This class is highly experimental. It has not been well tested and
     may disappear at any time.

Author(s):

     Michael Lawrence

See Also:

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

