mapCoords-methods {IRanges} | R Documentation |
DEFUNCT! Use mapToTranscripts
from the
GenomicFeatures package or
mapToAlignments
from the
GenomicAlignments package instead.
The mapCoords
generic converts a set of ranges to the equivalent
ranges on another sequence through some sort of alignment between
sequences. The output is an object of the same class as from
and in general will contain the mapped ranges with the matching data
as metadata. Matching data are the result of calling findOverlaps
with type = "within"
. This operation matches each input range to a
destination sequence (useful when the alignment is one/many to many).
The pmapCoords
function is simpler: it treats the two inputs as
parallel vectors, maps each input range via the corresponding alignment,
and returns the mapped ranges. There is one result per input element,
instead of the many-to-many result from mapCoords
.
mapCoords(from, to, ...) pmapCoords(from, to, ...)
from |
Typically an object containing ranges to map. |
to |
Typically an object representing an alignment. |
... |
Arguments to pass to methods |
An object the same class as from
.
In the case of mapCoords
, the result of findOverlaps
with type = “within“ are included as metadata columns ('queryHits'
and 'subjectHits').
Michael Lawrence
See ?`mapCoords-methods`
in the
GenomicRanges package for the mapCoords
method on
GRanges objects
See ?`mapCoords-methods`
in the
GenomicAlignments package for the mapCoords
method on
GAlignments objects
## DEFUNCT! See ?mapToTranscripts in the GenomicFeatures package and ## ?mapToAlignments in the GenomicAlignments package.