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bedr (version 1.1.5)

Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.

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Install

install.packages('bedr')

Monthly Downloads

1,457

Version

1.1.5

License

GPL-2

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Repository

https://github.com/theboutroslab/package-bedr

Maintainer

Paul Boutros

Last Published

January 24th, 2026

Functions in bedr (1.1.5)

cluster intervals

Query fasta sequence

Get adjacent flanks from regions

determine.input

Determine input format

is.merged.region

checks if region file is merged

convert a region index into a bed file dataframe

get.random.regions

generates a set of random regions

checks if regions in object a are found in object b

checks if regions in object a are found in object b

is.sorted.region

checks if region file is sorted

permute a set of regions

Gets the sort order of a region index similar to the order command

convert a vcf to a bedpe file

Plot venn diagram

Calculate the relative distance between two sets of intervals

write a vcf object

Get adjacent flanks from regions

Read a vcf into R

Get region size

verifies the reference sequence in a vcf

Interface to R's modifyList

get BEDPE ID from VCF ID

get BEDPE ID from VCF ID

Main bedtools wrapper function.

strsplit2matrix

split a vector of strings into tabular data

test.region.similarity

Compare sets of regions via jaccard and relative distance using permutation

calculate the jaccard distance between sets of intervals

get.example.regions

return a set of regions for the examples and unit testing

Data frame to list conversion

download.datasets

Download some useful datasets

gets the length of each chromosome for a species/build

convert a vcf to a bed file

is.valid.region

checks if region/index is valid

verifies that sequences are correct given coordinates and a reference

read a ucsc table into R

bedr.merge.region

merge i.e. collapse overlpaping regions

convert bed to vcf

create.tmp.bed.file

output R objects as tmpfiles

bedr.snm.region

sort a region file

outputs text if verbose flag is set

bedr.sort.region

sort a region file

bed dataframe to index string

checks if binary is in the path

Initialize some config settings for bedr

bedr.join.region

join two region objects using a left outer join

bedr.join.multiple.region

join multiple region objects

Main bedtools wrapper function.

bedr.plot.region

Visualize regions or intervals

bedr.subtract.region

subtracts features or ranges in object b from object a

adjust.coordinates

adjust coordinates for a BEDPE file

convert object to bed format