make_windows: Make windows along genome

In haizi-zh/bedtorch: R package for fast BED-file manipulation

Make windows along genome

Description

Make windows with the size of window_size along genome. Must provide genome so that intervals are restricted by chromosome sizes.

Usage

make_windows(window_size, genome, chrom = NULL)

Arguments

window_size	An integer value. Size of the windows in base pairs.
genome	Provide the genome identifier, e.g. GRCh37, hs37-1kg, or path/URL to the chromosome size file. Refer to GenomeInfoDb::Seqinfo() and read_bed().
chrom	A character vector. If provided, only generate windows for the specified chromosome(s).

Value

A GRanges object containing the generated windows.

Examples

# Generate 500kbp intervals for chr20 and chr22, GRCh38
result <- make_windows(window_size = 500e3L, genome = "GRCh38", chrom = c("20", "22"))
head(result)

# Generate 5Mbp intervals for all chromosomes of GRCh37 (default reference genome)
result <- make_windows(window_size = 5e6L, genome = "GRCh37")
head(result)

haizi-zh/bedtorch documentation built on July 1, 2022, 10:40 a.m.