bedr: Genomic Region Processing using Tools Such as BEDtools, BEDOPS and Tabix
Version 1.0.3

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bedr")

Popular man pages

bed2vcf: convert bed to vcf
bedr: Main bedtools wrapper function.
bedr.merge.region: merge i.e. collapse overlpaping regions
bedR-package: A bedtools wrapper for working with genomic ranges in R
read.vcf: Read a vcf into R
table2venn: Plot venn diagram
vcf2bed: convert a vcf to a bed file
See all...

All man pages Function index File listing

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

Functions

\%in.region\% Man page
bed2index Man page Source code
bed2vcf Man page Source code
bedr Man page Source code
bedr-package Man page Man page
bedr.join.multiple.region Man page Source code
bedr.join.region Man page Source code
bedr.merge.region Man page Source code
bedr.plot.region Man page Source code
bedr.setup Man page Source code
bedr.snm.region Man page Source code
bedr.sort.region Man page Source code
bedr.subtract.region Man page Source code
catv Man page Source code
check.binary Man page Source code
cluster.region Man page Source code
convert2bed Man page Source code
create.tmp.bed.file Man page Source code
determine.input Man page Source code
df2list Man page Source code
download.datasets Man page Source code
fill.vector Source code
fix.region Source code
flank.region Man page Source code
get.chr.length Man page Source code
get.example.regions Man page Source code
get.fasta Man page Source code
get.random.regions Man page Source code
grow.region Man page Source code
hash2vec Source code
in.region Man page Source code
index2bed Man page Source code
is.merged.region Man page Source code
is.sorted.region Man page Source code
is.valid.ref Man page Source code
is.valid.region Man page Source code
is.valid.seq Man page Source code
iterate.perm Source code
jaccard Man page Source code
modifyList2 Man page Source code
onAttach Source code
order.region Man page Source code
parse.vcf.header Source code
permute.region Man page Source code
process.input Man page Source code
query.ucsc Man page Source code
read.vcf Man page Source code
reldist Man page Source code
sample.interval Source code
size.region Man page Source code
strsplit2matrix Man page Source code
tabix Man page Source code
table2venn Man page Source code
test.region.similarity Man page Source code
vcf2bed Man page Source code
write.vcf Man page Source code

Files

inst
inst/tests
inst/tests/test.is.sorted.region.R
inst/tests/test.is.merged.region.R
inst/tests/test.determine.input.R
inst/tests/test.index2bed.R
inst/tests/test.process.input.R
inst/tests/test.tabix.R
inst/tests/test.convert2bed.R
inst/tests/test.is.valid.region.R
inst/tests/test.in.region.R
inst/tests/test.sort.region.R
inst/config
inst/config/config.yaml
inst/genomes
inst/genomes/human.hg18.genome
inst/genomes/human.hg19.genome
inst/genomes/mouse.mm8.genome
inst/genomes/mouse.mm9.genome
inst/genomes/human.hg38.genome
inst/extdata
inst/extdata/ucsc.hg19.example.fasta
inst/extdata/gap.sql
inst/extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz
inst/extdata/callerA.vcf.gz
inst/extdata/ucsc.hg19.RefSeq.chr1-2.txt.gz
inst/extdata/clinvar_dbSNP138_example.vcf.gz
inst/extdata/singleSampleOICR_example.vcf.gz
inst/extdata/multiSampleOICR_example.vcf.gz
inst/extdata/example-a-region.bed
inst/extdata/ucsc.hg19.example.fasta.fai
inst/extdata/CNA.segmented.txt.gz
inst/extdata/gap.txt.gz
inst/extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz.tbi
inst/extdata/rmsk.sql
inst/extdata/callerB.vcf.gz
inst/doc
inst/doc/Using-bedr.Rmd
inst/doc/Using-bedr.R
inst/doc/Using-bedr.html
tests
tests/test.all.R
NAMESPACE
NEWS
R
R/permute.region.R
R/get.chr.length.R
R/onAttach.R
R/tabix.R
R/bedr.R
R/order.region.R
R/jaccard.R
R/strsplit2matrix.R
R/process.input.R
R/download.datasets.R
R/vcf2bed.R
R/is.valid.region.R
R/test.region.similarity.R
R/is.sorted.region.R
R/is.valid.seq.R
R/get.example.regions.R
R/is.valid.ref.R
R/query.ucsc.R
R/determine.input.R
R/df2list.R
R/table2venn.R
R/bedr.plot.region.R
R/reldist.R
R/bed2index.R
R/get.random.regions.R
R/bedr.join.region.R
R/get.fasta.R
R/flank.region.R
R/is.merged.region.R
R/bedr.merge.region.R
R/bedr.sort.region.R
R/bed2vcf.R
R/catv.R
R/bedr.subtract.region.R
R/write.vcf.R
R/cluster.region.R
R/create.tmp.bed.file.R
R/read.vcf.R
R/bedr.join.multiple.region.R
R/check.binary.R
R/in.region.R
R/bedr.snm.region.R
R/modifyList2.R
R/grow.region.R
R/size.region.R
R/index2bed.R
R/convert2bed.R
R/bedr.setup.R
vignettes
vignettes/GitHub2.css
vignettes/Using-bedr.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/bed2index.Rd
man/table2venn.Rd
man/strsplit2matrix.Rd
man/download.datasets.Rd
man/bedr.setup.Rd
man/flank.region.Rd
man/bedr.join.multiple.region.Rd
man/bedr.Rd
man/is.valid.seq.Rd
man/check.binary.Rd
man/process.input.Rd
man/permute.region.Rd
man/in.region2.Rd
man/bedr.sort.region.Rd
man/write.vcf.Rd
man/test.region.similarity.Rd
man/read.vcf.Rd
man/catv.Rd
man/in.region.Rd
man/get.example.regions.Rd
man/cluster.region.Rd
man/order.region.Rd
man/bedr.join.region.Rd
man/bedr.plot.region.Rd
man/get.random.regions.Rd
man/bed2vcf.Rd
man/determine.input.Rd
man/get.fasta.Rd
man/convert2bed.Rd
man/grow.region.Rd
man/is.merged.region.Rd
man/is.valid.ref.Rd
man/bedr.merge.region.Rd
man/query.ucsc.Rd
man/modifyList2.Rd
man/jaccard.Rd
man/get.chr.length.Rd
man/tabix.Rd
man/is.sorted.region.Rd
man/create.tmp.bed.file.Rd
man/bedr.subtract.region.Rd
man/bedR-package.Rd
man/index2bed.Rd
man/size.region.Rd
man/is.valid.region.Rd
man/vcf2bed.Rd
man/df2list.Rd
man/bedr.snm.region.Rd
man/reldist.Rd
bedr documentation built on May 19, 2017, 10:48 p.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

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