%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
