map-methods {GenomicRanges} | R Documentation |
The GenomicRanges package provides several methods for the
map
generic. They each translate a set of input
ranges through a certain type of alignment and return a
RangesMapping
object.
## S4 method for signature 'GenomicRanges,GRangesList' map(from, to) ## S4 method for signature 'GenomicRanges,GappedAlignments' map(from, to)
from |
The input ranges to map, usually
a |
to |
The alignment between the sequences in |
The methods currently depend on the type of to
:
Each element is taken to represent an alignment
of a sequence on a genome. The typical case is a set of transcript
models, as might be obtained via
GenomicFeatures::exonsBy
. The method translates the input
ranges to be relative to the transcript start. This is useful, for
example, when predicting coding consequences of changes to the
genomic sequence.
Each element 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.
An object of class RangesMapping
. The GenomicRanges package
provides some additional methods on this object:
|
|
|
|
M. Lawrence
The RangesMapping
class is
the typical return value.