shuffle_bed: Shuffle intervals

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

Shuffle intervals

Description

This function randomly permutes genomic locations among a genome defined in a genome file. Note: the permutation stays in the same chromosome. Cross-chromosome shuffle is not supported at this point.

Usage

shuffle_bed(x, genome = NULL, excluded_region = NULL, sort = TRUE, seed = NULL)

Arguments

x	A GRanges.
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().
excluded_region	A GRanges containing regions that you don't want to exclude from the shuffle. Shuffled intervals are guaranteed not to fall within such regions.
sort	Logical value indicating whether to sort the shuffled features. When the input data set is large, sorting can be very expensive. If you don't need the output to be sorted, set sort to FALSE.
seed	An integer seed for the random number generator. If NULL, the seed is randomly chosen.

Value

A GRanges containing shuffled features.

References

Manual page of bedtools shuffle: https://bedtools.readthedocs.io/en/latest/content/tools/shuffle.html

Examples

# Load BED tables
tbl <- read_bed(system.file("extdata", "example_merge.bed", package = "bedtorch"), use_gr = FALSE, genome = "hs37-1kg")
excluded <- read_bed(system.file("extdata", "example_intersect_y.bed", package = "bedtorch"), use_gr = FALSE)

# Basic usage
result <- shuffle_bed(tbl)
head(result)

# Shuffle the data, but exclude certain regions. Plus, set the RNG seed to 1
result <- shuffle_bed(tbl, genome = "hs37-1kg", excluded_region = excluded, seed = 1)
head(result)

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