make_random_bed: Randomly place intervals of fixed width across genome

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

Randomly place intervals of fixed width across genome

Description

This function is aware of chromosome size differences and intervals are randomly generated in proportion to chromosome sizes. In another word, larger chromosomes will have more randomly generated intervals.

Usage

make_random_bed(
  n,
  interval_width,
  genome,
  chrom = NULL,
  seed = NULL,
  sort = TRUE
)

Arguments

n	Number of intervals to generate.
interval_width	An integer value of the width of the interval.
genome	Specify the reference genome for the BED file. genome can be a valid genome name in GenomeInfoDb::Seqinfo(), e.g. GRCh37, or hs37-1kg, which is a genome shipped with this package, or any custom chromosome size files (local or remote). If NULL, will try to obtain such information from input data. Refer to read_bed().
chrom	A character vector. If provided, only generate random intervals for the specified chromosome(s).
seed	An integer seed for the random number generator. If NULL, the seed is randomly chosen.
sort	Logical value. Should the random BED data be sorted?

Value

A GRanges of generated intervals.

References

Manual page for bedtools random: https://bedtools.readthedocs.io/en/latest/content/tools/random.html

Examples

# Generate 100 500kbp-intervals for chr20 and chr22, GRCh38
result <- make_random_bed(100, 500e3L, genome = "GRCh38", chrom = c("20", "22"))
head(result)

# Generate 100 500bp unsorted intervals for all chromosomes of GRCh37 (default reference genome)
result <- make_random_bed(100, interval_width = 500, genome = "GRCh37", sort = FALSE)
head(result)

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