Generate windows for a GenomicRanges
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.
## S4 method for signature 'GenomicRanges' tile(x, n, width) ## S4 method for signature 'GenomicRanges' slidingWindows(x, width, step=1L)
x |
A GenomicRanges object, like a |
n |
The number of tiles to generate.
See |
width |
The (maximum) width of each tile.
See |
step |
The distance between the start positions of the sliding windows. |
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.
A GRangesList object, each element of which corresponds to a window.
M. Lawrence
tile in the IRanges package.
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 truncatedPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.