# Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

## Documentation for package ‘bedr’ version 1.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

%in.region% | checks if regions in object a are found in object b
adjust.coordinates | adjust coordinates for a BEDPE file
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.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.bedpe.id | get BEDPE ID from VCF ID
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
get.strand | get BEDPE ID from VCF ID
grow.region | Get adjacent flanks from regions
in.region | checks if regions in object a are found in object b
index2bed | convert a region index into a bed file dataframe
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 reference
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 command
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 using permutation
vcf2bed | convert a vcf to a bed file
vcf2bedpe | convert a vcf to a bedpe file
write.vcf | write a vcf object