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

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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.

Author
Daryl Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros
Date of publication
2016-08-23 18:04:00
Maintainer
Paul Boutros <Paul.Boutros@oicr.on.ca>
License
GPL-2
Version
1.0.3

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