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bedr (version 1.1.3)

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

1,291

Version

1.1.3

License

GPL-2

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Repository

https://github.com/uclahs-cds/package-bedr

Maintainer

Paul C. Boutros

Last Published

April 6th, 2025

Functions in bedr (1.1.3)

Data frame to list conversion

outputs text if verbose flag is set

determine.input

Determine input format

cluster intervals

checks if regions in object a are found in object b

get BEDPE ID from VCF ID

download.datasets

Download some useful datasets

Query fasta sequence

Get adjacent flanks from regions

calculate the jaccard distance between sets of intervals

get.random.regions

generates a set of random regions

Interface to R's modifyList

gets the length of each chromosome for a species/build

Get adjacent flanks from regions

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

is.sorted.region

checks if region file is sorted

get BEDPE ID from VCF ID

verifies the reference sequence in a vcf

Read a vcf into R

convert a vcf to a bed file

bedr.sort.region

sort a region file

bedr.subtract.region

subtracts features or ranges in object b from object a

test.region.similarity

Compare sets of regions via jaccard and relative distance using permutation

Calculate the relative distance between two sets of intervals

get.example.regions

return a set of regions for the examples and unit testing

convert a region index into a bed file dataframe

write a vcf object

read a ucsc table into R

verifies that sequences are correct given coordinates and a reference

checks if regions in object a are found in object b

is.valid.region

checks if region/index is valid

is.merged.region

checks if region file is merged

convert a vcf to a bedpe file

strsplit2matrix

split a vector of strings into tabular data

Get region size

permute a set of regions

Plot venn diagram

Main bedtools wrapper function.

bed dataframe to index string

convert bed to vcf

bedr.snm.region

sort a region file

bedr.merge.region

merge i.e. collapse overlpaping regions

bedr.join.region

join two region objects using a left outer join

bedr.plot.region

Visualize regions or intervals

adjust.coordinates

adjust coordinates for a BEDPE file

create.tmp.bed.file

output R objects as tmpfiles

bedr.join.multiple.region

join multiple region objects

Initialize some config settings for bedr

convert object to bed format

Main bedtools wrapper function.

checks if binary is in the path