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bedr (version 1.0.1)

Genomic Region Processing using Tools Such as Bedtools, Bedops and Tabix

Description

Genomic region processing using tools such as bedtools, bedops and tabix.

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Version

Install

install.packages('bedr')

Monthly Downloads

958

Version

1.0.1

License

GPL-2

Maintainer

Paul Boutros

Last Published

September 5th, 2015

Functions in bedr (1.0.1)

tabix

Main bedtools wrapper function.

%in.region%

checks if regions in object a are found in object b

determine.input

Determine input format

download.datasets

Download some useful datasets

cluster.region

cluster intervals

is.sorted.region

checks if region file is sorted

bedr.merge.region

merge i.e. collapse overlpaping regions

convert2bed

convert object to bed format

write.vcf

write a vcf object

get.random.regions

generates a set of random regions

table2venn

Plot venn diagram

bedr.join.multiple.region

join multiple region objects

get.chr.length

gets the length of each chromosome for a species/build

permute.region

permute a set of regions

create.tmp.bed.file

output R objects as tmpfiles

flank.region

Get adjacent flanks from regions

jaccard

calculate the jaccard distance between sets of intervals

bedr.plot.region

Visualize regions or intervals

catv

outputs text if verbose flag is set

bedr.setup

Initialize some config settings for bedr

modifyList2

Interface to R's modifyList

check.binary

checks if binary is in the path

order.region

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

in.region

checks if regions in object a are found in object b

is.valid.region

checks if region/index is valid

bed2index

bed dataframe to index string

bedr.subtract.region

subtracts features or ranges in object b from object a

query.ucsc

read a ucsc table into R

verifies the reference sequence in a vcf

bedr-package

A bedtools wrapper for working with genomic ranges in R

process.input

grow.region

Get adjacent flanks from regions

index2bed

convert a region index into a bed file dataframe

bedr

Main bedtools wrapper function.

test.region.similarity

Compare sets of regions via jaccard and relative distance using permutation

bedr.join.region

join two region objects using a left outer join

vcf2bed

convert a vcf to a bed file

size.region

Get region size

is.merged.region

checks if region file is merged

split a vector of strings into tabular data

get.example.regions

return a set of regions for the examples and unit testing

is.valid.seq

verifies that sequences are correct given coordinates and a reference

reldist

Calculate the relative distance between two sets of intervals

snm

sort a region file

df2list

Data frame to list conversion