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 a 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). The pmap 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 map.

Usage

map(from, to, ...)
pmap(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 1.22.9 Index]