map-methods {GenomicRanges}R Documentation

Mapping ranges between sequences

Description

A method for translating a set of input ranges through a GRangesList object. Returns a RangesMapping object.

NOTE: The map generic function is defined and documented in the IRanges package. A method for translating a set of input ranges through a GAlignments object is defined and documented in the GenomicAlignments package.

Usage

## S4 method for signature 'GenomicRanges,GRangesList'
map(from, to)

Arguments

from

The input ranges to map, usually a GenomicRanges

to

The alignment between the sequences in from and the sequences in the result.

Details

Each element in to 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.

Value

An object of class RangesMapping. The GenomicRanges package provides some additional methods on this object:

as(from, "GenomicRanges"): Creates a GenomicRanges with seqnames and ranges from the space and ranges of from. The hits are coerced to a DataFrame and stored as the values of the result.

granges(x): Like the above, except returns just the range information as a GRanges, without the matching information.

Author(s)

M. Lawrence

See Also

The RangesMapping class is the typical return value.


[Package GenomicRanges version 1.16.3 Index]