bedr: Genomic Region Processing using Tools Such as BEDtools, BEDOPS and Tabix

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.

AuthorDaryl Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros
Date of publication2016-08-23 18:04:00
MaintainerPaul Boutros <Paul.Boutros@oicr.on.ca>
LicenseGPL-2
Version1.0.3

View on CRAN

Man pages

bed2index: bed dataframe to index string

bed2vcf: convert bed to vcf

bedr: Main bedtools wrapper function.

bedr.join.multiple.region: join multiple region objects

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

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

bedR-package: A bedtools wrapper for working with genomic ranges in R

bedr.plot.region: Visualize regions or intervals

bedr.setup: Initialize some config settings for bedr

bedr.snm.region: sort a region file

bedr.sort.region: sort a region file

bedr.subtract.region: subtracts features or ranges in object b from object a

catv: outputs text if verbose flag is set

check.binary: checks if binary is in the path

cluster.region: cluster intervals

convert2bed: convert object to bed format

create.tmp.bed.file: output R objects as tmpfiles

determine.input: Determine input format

df2list: Data frame to list conversion

download.datasets: Download some useful datasets

flank.region: Get adjacent flanks from 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

get.fasta: Query fasta sequence

get.random.regions: generates a set of random regions

grow.region: Get adjacent flanks from regions

index2bed: convert a region index into a bed file dataframe

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

in.region2: checks if regions in object a are found in object b

is.merged.region: checks if region file is merged

is.sorted.region: checks if region file is sorted

is.valid.ref: verifies the reference sequence in a vcf

is.valid.region: checks if region/index is valid

is.valid.seq: verifies that sequences are correct given coordinates and a...

jaccard: calculate the jaccard distance between sets of intervals

modifyList2: Interface to R's modifyList

order.region: Gets the sort order of a region index similar to the order...

permute.region: permute a set of regions

process.input: process.input

query.ucsc: read a ucsc table into R

read.vcf: Read a vcf into R

reldist: Calculate the relative distance between two sets of intervals

size.region: Get region size

strsplit2matrix: split a vector of strings into tabular data

tabix: Main bedtools wrapper function.

table2venn: Plot venn diagram

test.region.similarity: Compare sets of regions via jaccard and relative distance...

vcf2bed: convert a vcf to a bed file

write.vcf: write a vcf object

Files in this package

bedr
bedr/inst
bedr/inst/tests
bedr/inst/tests/test.is.sorted.region.R
bedr/inst/tests/test.is.merged.region.R
bedr/inst/tests/test.determine.input.R
bedr/inst/tests/test.index2bed.R
bedr/inst/tests/test.process.input.R
bedr/inst/tests/test.tabix.R
bedr/inst/tests/test.convert2bed.R
bedr/inst/tests/test.is.valid.region.R
bedr/inst/tests/test.in.region.R
bedr/inst/tests/test.sort.region.R
bedr/inst/config
bedr/inst/config/config.yaml
bedr/inst/genomes
bedr/inst/genomes/human.hg18.genome
bedr/inst/genomes/human.hg19.genome
bedr/inst/genomes/mouse.mm8.genome
bedr/inst/genomes/mouse.mm9.genome
bedr/inst/genomes/human.hg38.genome
bedr/inst/extdata
bedr/inst/extdata/ucsc.hg19.example.fasta
bedr/inst/extdata/gap.sql
bedr/inst/extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz
bedr/inst/extdata/callerA.vcf.gz
bedr/inst/extdata/ucsc.hg19.RefSeq.chr1-2.txt.gz
bedr/inst/extdata/clinvar_dbSNP138_example.vcf.gz
bedr/inst/extdata/singleSampleOICR_example.vcf.gz
bedr/inst/extdata/multiSampleOICR_example.vcf.gz
bedr/inst/extdata/example-a-region.bed
bedr/inst/extdata/ucsc.hg19.example.fasta.fai
bedr/inst/extdata/CNA.segmented.txt.gz
bedr/inst/extdata/gap.txt.gz
bedr/inst/extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz.tbi
bedr/inst/extdata/rmsk.sql
bedr/inst/extdata/callerB.vcf.gz
bedr/inst/doc
bedr/inst/doc/Using-bedr.Rmd
bedr/inst/doc/Using-bedr.R
bedr/inst/doc/Using-bedr.html
bedr/tests
bedr/tests/test.all.R
bedr/NAMESPACE
bedr/NEWS
bedr/R
bedr/R/permute.region.R bedr/R/get.chr.length.R bedr/R/onAttach.R bedr/R/tabix.R bedr/R/bedr.R bedr/R/order.region.R bedr/R/jaccard.R bedr/R/strsplit2matrix.R bedr/R/process.input.R bedr/R/download.datasets.R bedr/R/vcf2bed.R bedr/R/is.valid.region.R bedr/R/test.region.similarity.R bedr/R/is.sorted.region.R bedr/R/is.valid.seq.R bedr/R/get.example.regions.R bedr/R/is.valid.ref.R bedr/R/query.ucsc.R bedr/R/determine.input.R bedr/R/df2list.R bedr/R/table2venn.R bedr/R/bedr.plot.region.R bedr/R/reldist.R bedr/R/bed2index.R bedr/R/get.random.regions.R bedr/R/bedr.join.region.R bedr/R/get.fasta.R bedr/R/flank.region.R bedr/R/is.merged.region.R bedr/R/bedr.merge.region.R bedr/R/bedr.sort.region.R bedr/R/bed2vcf.R bedr/R/catv.R bedr/R/bedr.subtract.region.R bedr/R/write.vcf.R bedr/R/cluster.region.R bedr/R/create.tmp.bed.file.R bedr/R/read.vcf.R bedr/R/bedr.join.multiple.region.R bedr/R/check.binary.R bedr/R/in.region.R bedr/R/bedr.snm.region.R bedr/R/modifyList2.R bedr/R/grow.region.R bedr/R/size.region.R bedr/R/index2bed.R bedr/R/convert2bed.R bedr/R/bedr.setup.R
bedr/vignettes
bedr/vignettes/GitHub2.css
bedr/vignettes/Using-bedr.Rmd
bedr/MD5
bedr/build
bedr/build/vignette.rds
bedr/DESCRIPTION
bedr/man
bedr/man/bed2index.Rd bedr/man/table2venn.Rd bedr/man/strsplit2matrix.Rd bedr/man/download.datasets.Rd bedr/man/bedr.setup.Rd bedr/man/flank.region.Rd bedr/man/bedr.join.multiple.region.Rd bedr/man/bedr.Rd bedr/man/is.valid.seq.Rd bedr/man/check.binary.Rd bedr/man/process.input.Rd bedr/man/permute.region.Rd bedr/man/in.region2.Rd bedr/man/bedr.sort.region.Rd bedr/man/write.vcf.Rd bedr/man/test.region.similarity.Rd bedr/man/read.vcf.Rd bedr/man/catv.Rd bedr/man/in.region.Rd bedr/man/get.example.regions.Rd bedr/man/cluster.region.Rd bedr/man/order.region.Rd bedr/man/bedr.join.region.Rd bedr/man/bedr.plot.region.Rd bedr/man/get.random.regions.Rd bedr/man/bed2vcf.Rd bedr/man/determine.input.Rd bedr/man/get.fasta.Rd bedr/man/convert2bed.Rd bedr/man/grow.region.Rd bedr/man/is.merged.region.Rd bedr/man/is.valid.ref.Rd bedr/man/bedr.merge.region.Rd bedr/man/query.ucsc.Rd bedr/man/modifyList2.Rd bedr/man/jaccard.Rd bedr/man/get.chr.length.Rd bedr/man/tabix.Rd bedr/man/is.sorted.region.Rd bedr/man/create.tmp.bed.file.Rd bedr/man/bedr.subtract.region.Rd bedr/man/bedR-package.Rd bedr/man/index2bed.Rd bedr/man/size.region.Rd bedr/man/is.valid.region.Rd bedr/man/vcf2bed.Rd bedr/man/df2list.Rd bedr/man/bedr.snm.region.Rd bedr/man/reldist.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.