RangedSelection-class        package:IRanges        R Documentation

Selection of ranges and columns

Description:

     A 'RangedSelection' represents a query against a table of interval
     data in terms of ranges and column names. The ranges select any
     table row with an overlapping interval. Note that the intervals
     are always returned, even if no columns are selected.

Details:

     Traditionally, tabular data structures have supported the 'subset'
     function, which allows one to select a subset of the rows and
     columns from the table. In that case, the rows and columns are
     specified by two separate arguments. As querying interval data
     sources, especially those external to R, such as binary indexed
     files and databases, is increasingly common, there is a need to
     encapsulate the row and column specifications into a single data
     structure, mostly for the sake of interface cleanliness. The
     'RangedSelection' class fills that role.

Constructor:


      'RangedSelection(ranges = RangesList(), colnames = character())':
          Constructors a 'RangedSelection' with the given 'ranges' and
          'colnames'.


Coercion:


      'as(from, "RangedSelection")': Coerces 'from' to a
          'RangedSelection' object. Typically, 'from' is a
          'RangesList', the ranges of which become the ranges in the
          new 'RangedSelection'.


Accessors:

     In the code snippets below, 'x' is always a 'RangedSelection'.

      'ranges(x), ranges(x) <- value': Gets or sets the ranges, a
          'RangesList', that select rows with overlapping intervals.

      'colnames(x), colnames(x) <- value': Gets the  names, a
          'character' vector, indicating the columns.


Author(s):

     Michael Lawrence

Examples:

       rl <- RangesList(chr1 = IRanges(c(1, 5), c(3, 6)))

       RangedSelection(rl)
       as(rl, "RangedSelection") # same as above

       RangedSelection(rl, "score")

