GRangesMapping objects

Description

The GRangesMapping class is a container for both the genomic locations and the matching results output from the map function.

Details

The map generic converts a set of ranges to the equivalent ranges on another sequence, through some sort of alignment between sequences, and outputs a GRangesMapping object. There are two components of that object: the transformed GRanges, and the hits, a Hits object of the same length that matches each input range to a destination sequence (useful when the alignment is one/many to many).

GRangesMapping Accessors

granges(x): Gets the mapped GRanges.

hits(x): Gets the matching between the input ranges and the destination sequences (of which there may be more than one).

dim(x): Same as dim(hits(x)).

length(x): Same as length(hits(x)).

subjectHits(x): Same as subjectHits(hits(x)).

queryHits(x): Same as queryHits(hits(x)).

GRangesMapping Coercion

as(from, "RangedData"): Converts a GRangesMapping into a RangedData. The ranges/space in the RangedData are the ranges/space of from, and the values result from the coercion of the hits to a DataFrame.

as(from, "GenomicRanges"): Returns the GRanges with the hits (coerced to a DataFrame) as the mcols.

Author(s)

Michael Lawrence

See Also

Methods on the generic map, which generates an instance of this class, are defined in other packages, like GenomicRanges.

Examples

# See ?map-methods in GenomicRanges or GenomicAlignments for examples.