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bedr (version 1.0.0)

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

1.0.0

License

GPL-2

Maintainer

Paul Boutros

Last Published

September 4th, 2015

Functions in bedr (1.0.0)

bedr

Main bedtools wrapper function.

catv

outputs text if verbose flag is set

bedr-package

A bedtools wrapper for working with genomic ranges in R

bedr.sort.region

sort a region file

get.chr.length

gets the length of each chromosome for a species/build

read.vcf

Read a vcf into R

is.valid.ref

verifies the reference sequence in a vcf

bedr.merge.region

merge i.e. collapse overlpaping regions

cluster.region

cluster intervals

reldist

Calculate the relative distance between two sets of intervals

create.tmp.bed.file

output R objects as tmpfiles

bedr.setup

Initialize some config settings for bedr

query.ucsc

read a ucsc table into R

get.example.regions

return a set of regions for the examples and unit testing

bedr.subtract.region

subtracts features or ranges in object b from object a

convert2bed

convert object to bed format

modifyList2

Interface to R's modifyList

%in.region%

checks if regions in object a are found in object b

determine.input

Determine input format

grow.region

Get adjacent flanks from regions

check.binary

checks if binary is in the path

process.input

df2list

Data frame to list conversion

is.sorted.region

checks if region file is sorted

snm

sort a region file

test.region.similarity

Compare sets of regions via jaccard and relative distance using permutation

get.fasta

Query fasta sequence

get.random.regions

generates a set of random regions

is.valid.region

checks if region/index is valid

strsplit2matrix

split a vector of strings into tabular data

is.valid.seq

verifies that sequences are correct given coordinates and a reference

is.merged.region

checks if region file is merged

write.vcf

write a vcf object

tabix

Main bedtools wrapper function.

flank.region

Get adjacent flanks from regions

bedr.plot.region

Visualize regions or intervals

jaccard

calculate the jaccard distance between sets of intervals

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

index2bed

convert a region index into a bed file dataframe

table2venn

Plot venn diagram

vcf2bed

convert a vcf to a bed file

bed2vcf

convert bed to vcf

bedr.join.multiple.region

join multiple region objects

bedr.join.region

join two region objects using a left outer join

bed2index

bed dataframe to index string

download.datasets

Download some useful datasets

permute.region

permute a set of regions

size.region

Get region size