IRanges (version 2.0.1)

mapCoords-methods: Mapping of ranges to another sequence

Description

The mapCoords generic converts a set of ranges to the equivalent ranges on another sequence through some sort of alignment between sequences. The output is an object of the same class as x and in general will contain the mapped ranges with the matching data as metadata. Matching data are the result of calling findOverlaps with type = "within". This operation matches each input range to a destination sequence (useful when the alignment is one/many to many).

The pmapCoords 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 mapCoords.

Usage

mapCoords(x, to, ...)
pmapCoords(x, to, ...)

Arguments

x

Typically an object containing ranges to map.

to

Typically an object representing an alignment.

...

Arguments to pass to methods

Value

An object the same class as x.In the case of mapCoords, the result of findOverlaps with type = ``within`` are inlcuded as metadata columns (`queryHits` and `subjectHits`).

See Also

• See ?`mapCoords-methods` in the GenomicRanges package for the mapCoords method on GRanges objects
• See ?`mapCoords-methods` in the GenomicAlignments package for the mapCoords method on GAlignments objects

Examples

## See mapCoords methods in GenomicRanges and GAlignmentsPackages.