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bedr (version 1.0.2)

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

1.0.2

License

GPL-2

Maintainer

Paul Boutros

Last Published

September 21st, 2015

Functions in bedr (1.0.2)

bed2index

bed dataframe to index string

cluster.region

cluster intervals

flank.region

Get adjacent flanks from regions

bedr

Main bedtools wrapper function.

determine.input

Determine input format

get.chr.length

gets the length of each chromosome for a species/build

bedr.setup

Initialize some config settings for bedr

bedr.plot.region

Visualize regions or intervals

create.tmp.bed.file

output R objects as tmpfiles

convert object to bed format

bedr.merge.region

merge i.e. collapse overlpaping regions

permute.region

permute a set of regions

jaccard

calculate the jaccard distance between sets of intervals

read.vcf

Read a vcf into R

bedr-package

A bedtools wrapper for working with genomic ranges in R

snm

sort a region file

bedr.subtract.region

subtracts features or ranges in object b from object a

is.merged.region

checks if region file is merged

strsplit2matrix

split a vector of strings into tabular data

process.input

is.sorted.region

checks if region file is sorted

size.region

Get region size

bedr.join.region

join two region objects using a left outer join

check.binary

checks if binary is in the path

vcf2bed

convert a vcf to a bed file

bedr.join.multiple.region

join multiple region objects

df2list

Data frame to list conversion

grow.region

Get adjacent flanks from regions

catv

outputs text if verbose flag is set

test.region.similarity

Compare sets of regions via jaccard and relative distance using permutation

get.example.regions

return a set of regions for the examples and unit testing

reldist

Calculate the relative distance between two sets of intervals

modifyList2

Interface to R's modifyList

get.fasta

Query fasta sequence

order.region

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

query.ucsc

read a ucsc table into R

is.valid.region

checks if region/index is valid

index2bed

convert a region index into a bed file dataframe

%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

tabix

Main bedtools wrapper function.

is.valid.ref

verifies the reference sequence in a vcf

get.random.regions

generates a set of random regions

is.valid.seq

verifies that sequences are correct given coordinates and a reference

write.vcf

write a vcf object

download.datasets

Download some useful datasets

table2venn

Plot venn diagram