range-squeezers {IRanges} | R Documentation

## Squeeze the ranges out of a range-based object

### Description

S4 generic functions for squeezing the ranges out of a range-based object.

These are analog to range squeezers `granges` and `grglist` defined in the GenomicRanges package, except that `ranges` returns the ranges in an IRanges object (instead of a GRanges object for `granges`), and `rglist` returns them in an IRangesList object (instead of a GRangesList object for `grglist`).

### Usage

    ranges(x, use.names=TRUE, use.mcols=FALSE, ...)
    rglist(x, use.names=TRUE, use.mcols=FALSE, ...)

### Arguments

`x` | An object containing ranges e.g. a IntegerRanges, GenomicRanges, RangedSummarizedExperiment, GAlignments, GAlignmentPairs, or GAlignmentsList object, or a Pairs object containing ranges.
`use.names` | `TRUE` (the default) or `FALSE`. Whether or not the names on `x` (accessible with `names(x)`) should be propagated to the returned object.
`use.mcols` | `TRUE` or `FALSE` (the default). Whether or not the metadata columns on `x` (accessible with `mcols(x)`) should be propagated to the returned object.
`...` | Additional arguments, for use in specific methods.

### Details

Various packages (e.g. IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments, etc...) define and document various range squeezing methods for various types of objects.

Note that these functions can be seen as object getters or as functions performing coercion.

For some objects (e.g. GAlignments and GAlignmentPairs objects defined in the GenomicAlignments package), `as(x, "IRanges")` and `as(x, "IRangesList")`, are equivalent to `ranges(x, use.names=TRUE, use.mcols=TRUE)` and `rglist(x, use.names=TRUE, use.mcols=TRUE)`, respectively.

### Value

An IRanges object for `ranges`.

An IRangesList object for `rglist`.

If `x` is a vector-like object (e.g. GAlignments), the returned object is expected to be parallel to `x`, that is, the i-th element in the output corresponds to the i-th element in the input.

If `use.names` is TRUE, then the names on `x` (if any) are propagated to the returned object. If `use.mcols` is TRUE, then the metadata columns on `x` (if any) are propagated to the returned object.

### Author(s)

H. Pagès

### See Also

- IRanges and IRangesList objects.

- RangedSummarizedExperiment objects in the SummarizedExperiment packages.

- GAlignments, GAlignmentPairs, and GAlignmentsList objects in the GenomicAlignments package.

### Examples

    ## See ?GAlignments in the GenomicAlignments package for examples of
    ## "ranges" and "rglist" methods.

[Package IRanges version 2.14.12 Index]