IMPORTANT NOTE - 9/4/2014: This man page is being refactored. Most of the things that used to be documented here have been moved to the man page for List objects located in the S4Vectors package.
The NCList class is a container for storing the Nested Containment List representation of a Ranges object. Preprocessing a Ranges object as a Nested Containment List allows efficient overlap-based operations like findOverlaps.
IMPORTANT NOTE: Starting with BioC 3.3, RangedDataList objects are deprecated in favor of GRangesList objects (the GRangesList class is defined in the GenomicRanges package). Note that the use of RangedData and RangedDataList objects has been discouraged in favor of GRanges and GRangesList objects since BioC 2.12.
IMPORTANT NOTE: Starting with BioC 3.3, RangedDataList objects are deprecated in favor of GRangesList objects (the GRangesList class is defined in the GenomicRanges package). Note that the use of RangedData and RangedDataList objects has been discouraged in favor of GRanges and GRangesList objects since BioC 2.12.
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.
An extension of List that holds only Ranges objects. Useful for storing ranges over a set of spaces (e.g. chromosomes), each of which requires a separate Ranges object. As a Vector, RangesList may be annotated with its universe identifier (e.g. a genome) in which all of its spaces exist.
providing 
.