RangesMapping-class {IRanges}R Documentation

Mapping of ranges to another sequence

Description

The map generic converts a set of ranges to the equivalent ranges on another sequence, through some sort of alignment between sequences, and outputs an RangesMapping object. There are three primary components of that object: the transformed ranges, the space (destination sequence) for the ranges, 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).

Usage

map(from, to, ...)

Arguments

from

Typically an object containing ranges to map.

to

Typically an object representing an alignment.

...

Arguments to pass to methods

Value

A RangesMapping object, as documented here.

RangesMapping Accessors

ranges(x): Gets the mapped ranges.

space(x): Gets the destination spaces (sequence names).

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)).

RangesMapping Coercion

as(from, "RangedData"): Converts a RangesMapping 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.

Author(s)

Michael Lawrence

See Also

Methods on the generic map, which generates an instance of this class, are defined in other packages, like GenomicRanges.


[Package IRanges version 1.14.4 Index]