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bedr (version 1.0.7)

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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Version

Install

install.packages('bedr')

Monthly Downloads

1,291

Version

1.0.7

License

GPL-2

Maintainer

Paul C. Boutros

Last Published

April 1st, 2019

Functions in bedr (1.0.7)

bedr-package

A bedtools wrapper for working with genomic ranges in R
is.merged.region

checks if region file is merged
df2list

Data frame to list conversion
catv

outputs text if verbose flag is set
bedr.merge.region

merge i.e. collapse overlpaping regions
bedr.plot.region

Visualize regions or intervals
download.datasets

Download some useful datasets
bedr.join.multiple.region

join multiple region objects
is.sorted.region

checks if region file is sorted
bedr.join.region

join two region objects using a left outer join
bedr.sort.region

sort a region file
check.binary

checks if binary is in the path
bed2index

bed dataframe to index string
is.valid.ref

verifies the reference sequence in a vcf
size.region

Get region size
process.input

process.input
strsplit2matrix

split a vector of strings into tabular data
bedr.setup

Initialize some config settings for bedr
bed2vcf

convert bed to vcf
%in.region%

checks if regions in object a are found in object b
in.region

checks if regions in object a are found in object b
order.region

Gets the sort order of a region index similar to the order command
bedr.snm.region

sort a region file
create.tmp.bed.file

output R objects as tmpfiles
determine.input

Determine input format
flank.region

Get adjacent flanks from regions
bedr.subtract.region

subtracts features or ranges in object b from object a
permute.region

permute a set of regions
get.chr.length

gets the length of each chromosome for a species/build
get.example.regions

return a set of regions for the examples and unit testing
write.vcf

write a vcf object
query.ucsc

read a ucsc table into R
get.random.regions

generates a set of random regions
get.fasta

Query fasta sequence
tabix

Main bedtools wrapper function.
jaccard

calculate the jaccard distance between sets of intervals
grow.region

Get adjacent flanks from regions
test.region.similarity

Compare sets of regions via jaccard and relative distance using permutation
vcf2bed

convert a vcf to a bed file
table2venn

Plot venn diagram
is.valid.region

checks if region/index is valid
modifyList2

Interface to R's modifyList
read.vcf

Read a vcf into R
is.valid.seq

verifies that sequences are correct given coordinates and a reference
reldist

Calculate the relative distance between two sets of intervals
cluster.region

cluster intervals
convert2bed

convert object to bed format
index2bed

convert a region index into a bed file dataframe
bedr

Main bedtools wrapper function.