tile-methods {GenomicRanges} | R Documentation

## Generate windows for a GenomicRanges

### Description

`tile` and `slidingWindows` methods for GenomicRanges. `tile` partitions each range into a set of tiles, which are defined in terms of their number or width. `slidingWindows` generates sliding windows of a specified width and frequency.

### Usage

    ## S4 method for signature 'GenomicRanges'
    tile(x, n, width)
    ## S4 method for signature 'GenomicRanges'
    slidingWindows(x, width, step=1L)

### Arguments

`x` | A GenomicRanges object, like a `GRanges`.
`n` | The number of tiles to generate. See `?tile` in the IRanges package for more information about this argument.
`width` | The (maximum) width of each tile. See `?tile` in the IRanges package for more information about this argument.
`step` | The distance between the start positions of the sliding windows.

### Details

The `tile` function splits `x` into a `GRangesList`, each element of which corresponds to a tile, or partition, of `x`. Specify the tile geometry with either `n` or `width` (not both). Passing `n` creates `n` tiles of approximately equal width, truncated by sequence end, while passing `width` tiles the region with ranges of the given width, again truncated by sequence end.

The `slidingWindows` function generates sliding windows within each range of `x`, according to `width` and `step`, returning a `GRangesList`. If the sliding windows do not exactly cover a range in `x`, the last window is partial.

### Value

A `GRangesList` object, each element of which corresponds to a window.

### Author(s)

M. Lawrence

### See Also

`tile` in the IRanges package.

### Examples

    gr <- GRanges(
            seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
            ranges=IRanges(1:10, end=11),
            strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
            seqlengths=c(chr1=11, chr2=12, chr3=13))

    # split every range in half
    tiles <- tile(gr, n = 2L)
    stopifnot(all(elementNROWS(tiles) == 2L))

    # split ranges into subranges of width 2
    # odd width ranges must contain one subrange of width 1
    tiles <- tile(gr, width = 2L)
    stopifnot(all(all(width(tiles) %in% c(1L, 2L))))

    windows <- slidingWindows(gr, width=3L, step=2L)
    width(windows[[1L]]) # last range is truncated

[Package GenomicRanges version 1.39.3 Index]