GenomicAlignments (version 1.4.2)

mapCoords-methods: Mapping ranges between sequences

Description

DEPRECATED! Use mapToAlignments instead.

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

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

Usage

"mapCoords"(from, to, ...)

Arguments

from

The input ranges to map, usually a GRanges.

to

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

...

Arguments passed to other methods.

Value

A GRanges object of mapped coordinates with matching data as metadata columns (`fromHits` and `toHits`).Matching data are the result of calling findOverlaps with type `within` on ranges in from (the query) and the ranges in to (the subject). Matching can be many-to-one or one-to-many; one row is reported for each match.

Details

DEPRECATED! Use mapToAlignments instead.

Each element in to is taken to represent the alignment of a (read) sequence. The CIGAR string is used to translate the input ranges to be relative to the read start. This is useful, for example, when determining the cycle (read position) at which a particular genomic mismatch occurs.

See Also

The generic mapCoords-methods in the IRanges package. Additional methods in the GenomicRanges package mapCoords-methods.

Examples

## DEPRECATED! See ?mapToAlignments for a replacement.