| mapCoords-methods {GenomicAlignments} | R Documentation |
DEPRECATED! Use mapToAlignments instead.
A method for translating a set of input ranges through a GAlignments object. Returns a GenomicRanges object.
NOTE: The mapCoords generic function is
defined and documented in the IRanges package. A method for
translating a set of input ranges through a
GRangesList object is defined and documented
in the GenomicRanges package.
## S4 method for signature 'GenomicRanges,GAlignments' mapCoords(from, to, ...)
from |
The input ranges to map, usually a |
to |
The alignment between the sequences in |
... |
Arguments passed to other methods. |
DEPRECATED! Use mapToAlignments instead.
Each element in to is taken to represent the
alignment of a (read) sequence. The CIGAR string is used to
translate the input ranges to be relative to the read start. This
is useful, for example, when determining the cycle (read position)
at which a particular genomic mismatch occurs.
A GRanges object of mapped coordinates with matching data
as metadata columns ('fromHits' and 'toHits').
Matching data are the result of calling findOverlaps with
type 'within' on ranges in from (the query) and the
ranges in to (the subject). Matching can be many-to-one
or one-to-many; one row is reported for each match.
M. Lawrence
The generic mapCoords-methods in the IRanges package. Additional methods in the GenomicRanges package mapCoords-methods.
## DEPRECATED! See ?mapToAlignments for a replacement.