The GRangesMapping class is a container for both the genomic
locations and the matching results output from the map
function.
Arguments
<code>GRangesMapping</code> 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)).
<code>GRangesMapping</code> 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.
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).
See Also
Methods on the generic map, which generates an instance of
this class, are defined in other packages, like GenomicRanges.