mapCoords-methods {GenomicRanges}R Documentation

Mapping ranges between sequences

Description

DEPRECATED! Use mapToTranscripts from the GenomicFeatures package or mapToAlignments from the GenomicAlignments package instead.

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

The generics for mapCoords and pmapCoords are defined in the IRanges package. A method for translating a set of input ranges through a GAlignments object is defined and in the GenomicAlignments package.

Usage

## S4 method for signature 'GenomicRanges,GRangesList'
mapCoords(from, to, ..., 
          ignore.strand = TRUE, elt.hits = FALSE)

## S4 method for signature 'GenomicRanges,GRangesList'
pmapCoords(from, to, ..., 
          ignore.strand = TRUE, elt.hits = FALSE)

Arguments

from

The input ranges to map, usually a GRanges.

to

The alignment between the sequences in from and the sequences in the result, usually a GRangesList.

ignore.strand

logical; When TRUE strand is ignored in overlap operations.

elt.hits

logical; When TRUE, the output includes a metadata column, eltHits, with indices of the inner list elements of to hit by from. Useful for identifying elements of to hit by from. See examples.

...

Arguments passed to other methods. Currently not used.

Details

DEPRECATED! Use mapToTranscripts from the GenomicFeatures package or mapToAlignments from the GenomicAlignments package instead.

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. Each outer list element of the GRangesList represents a transcript while each each individual element is an exon in the transcript.

mapCoords and pmapCoords translate the ranges in from relative to the transcript start (i.e., start of all ranges in to). The widths of the individual elements (exons in this example) are concatenated and counting starts at the 5' or 3' end depending on strand. Translated coordinates are only reported for ranges in from that fall completely 'within' ranges in to.

The transcript-centric coordinates are are useful, for example, when predicting coding consequences of changes to the genomic sequence.

mapCoords maps the i-th element in from to each element in to returning in a many-to-many mapping. In contrast, pmapCoords treats the two inputs as parallel vectors and maps the i-th element of from to the i-th element of to returning a maximum of one result per input element.

Value

A GRanges object of mapped coordinates with matching data as metadata columns fromHits and toHits. The ranges in the output GRanges are position relative to the outer list element of to; all individual list elements are concatenated and counting starts at the 5' or 3' end depending on strand.

Matching data are the result of calling findOverlaps with type 'within' on ranges in from (the query) and the ranges in to (the subject). In the case of mapCoords matching can be many-to-one or one-to-many; one row is reported for each match. For pmapCoords matching is one-to-one as the i-th element in from is only mapped to the i-th element in to.

When elt.hits is TRUE, the eltHits metadata column includes the index of inner list elements in to hit by from. In some applications it may be useful to identify the exact list element that was overlapped. These elements can be extracted with the combination of toHits (outer list index) and eltHits (inner list index).

Author(s)

M. Lawrence and V. Obenchain vobencha@fhcrc.org

See Also

Examples

## DEPRECATED! See ?mapToTranscripts in the GenomicFeatures package and
## ?mapToAlignments in the GenomicAlignments package.

[Package GenomicRanges version 1.20.3 Index]