Flexibly bin ranges
Usage
binRanges(x, binSize, pos = "center")
# S4 method for GRanges,numeric,character_OR_numeric_OR_missing
binRanges(x, binSize, pos = "center")Arguments
- x
`GRanges` object
- binSize
Integer (numeric) describing the new size of each range.
- pos
Position within range to resize the bin. Can be a character or integer vector of length 1 or `length(x)` designating the position for each element in `x`. Character options are "start", "end" and "center". Integers are referenced from the start position for '+' and '*' strands and from the end position for the '-' strand.
Examples
library(GenomicRanges)
## Create example GRanges
gr1 <- GRanges(seqnames = "chr1",
ranges = IRanges::IRanges(start = rep(5000,3),
end = rep(6000,3)),
strand = c('+', '-', '*'))
gr2 <- gr1 |> promoters(upstream = 2000, downstream = 200)
## Binning the results
binRanges(x = gr1, binSize = 1000, pos = 'start')
#> GRanges object with 3 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 5000-6000 +
#> [2] chr1 6000-7000 -
#> [3] chr1 5000-6000 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
binRanges(x = gr1, binSize = 1000, pos = 'end')
#> GRanges object with 3 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 6000-7000 +
#> [2] chr1 5000-6000 -
#> [3] chr1 6000-7000 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
binRanges(x = gr1, binSize = 1000, pos = 'center')
#> GRanges object with 3 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 5000-6000 +
#> [2] chr1 5000-6000 -
#> [3] chr1 5000-6000 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Bin after shifting back to TSS
binRanges(x = gr2, binSize = 1000, pos = 2000)
#> GRanges object with 3 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 5000-6000 +
#> [2] chr1 6000-7000 -
#> [3] chr1 5000-6000 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths