The DelegatingGenomicRanges class implements the virtual GenomicRanges class using a delegate GenomicRanges. This enables developers to create GenomicRanges subclasses that add specialized columns or other structure, while remaining agnostic to how the data are actually stored. See the Extending GenomicRanges vignette.
The GNCList class is a container for storing the Nested Containment List representation of a vector of genomic ranges (typically represented as a GRanges object). To preprocess a GRanges object, simply call the GNCList constructor function on it. The resulting GNCList object can then be used for efficient overlap-based operations on the genomic ranges.
The GPos class is a container for storing a set of genomic positions, that is, genomic ranges of width 1. Even though a GRanges object can be used for that, using a GPos object can be much more memory-efficient, especially when the object contains long runs of adjacent positions.
A GenomicRangesList is a List of GenomicRanges. It is a virtual class; SimpleGenomicRangesList is the basic implementation. The subclass GRangesList provides special behavior and is particularly efficient for storing a large number of elements.
absoluteRanges transforms the genomic ranges in x into absolute ranges i.e. into ranges counted from the beginning of the virtual sequence obtained by concatenating all the sequences in the underlying genome (in the order reported by seqlevels(x)).
Attaching a Constraint object to an object of class A (the "constrained" object) is meant to be a convenient/reusable/extensible way to enforce a particular set of constraints on particular instances of A.
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