Slide or tile over a Ranges object
tile_ranges(x, width)
slide_ranges(x, width, step)a Ranges object
the maximum width of each window/tile (integer vector of length 1)
the distance between start position of each sliding window (integer vector of length 1)
a Ranges object
The tile_ranges() function paritions a Ranges object x by the given the
width over all ranges in x, truncated by the sequence end.
The slide_ranges() function makes sliding windows within each range of x
of size width and sliding by step.
Both slide_ranges() and tile_ranges() return a new Ranges object
with a metadata column called "partition" which contains the index of the
input range x that a parition belongs to.
GenomicRanges::tile()
gr <- data.frame(seqnames = c("chr1", rep("chr2", 3), rep("chr1", 2), rep("chr3", 4)),
start = 1:10,
end = 11,
strand = c("-", rep("+", 2), rep("*", 2), rep("+", 3), rep("-", 2))) %>%
as_granges() %>%
set_genome_info(seqlengths = c(11,12,13))
# partition ranges into subranges of width 2, odd width ranges
# will have one subrange of width 1
tile_ranges(gr, width = 2)
#> GRanges object with 35 ranges and 1 metadata column:
#> seqnames ranges strand | partition
#> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 1 - | 1
#> [2] chr1 2-3 - | 1
#> [3] chr1 4-5 - | 1
#> [4] chr1 6-7 - | 1
#> [5] chr1 8-9 - | 1
#> ... ... ... ... . ...
#> [31] chr3 8-9 + | 8
#> [32] chr3 10-11 + | 8
#> [33] chr3 9 - | 9
#> [34] chr3 10-11 - | 9
#> [35] chr3 10-11 - | 10
#> -------
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths
# make sliding windows of width 3, moving window with step size of 2
slide_ranges(gr, width = 3, step = 2)
#> GRanges object with 30 ranges and 1 metadata column:
#> seqnames ranges strand | partition
#> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 1-3 - | 1
#> [2] chr1 3-5 - | 1
#> [3] chr1 5-7 - | 1
#> [4] chr1 7-9 - | 1
#> [5] chr1 9-11 - | 1
#> ... ... ... ... . ...
#> [26] chr3 9-11 + | 7
#> [27] chr3 8-10 + | 8
#> [28] chr3 10-11 + | 8
#> [29] chr3 9-11 - | 9
#> [30] chr3 10-11 - | 10
#> -------
#> seqinfo: 3 sequences from an unspecified genome