A bedtools wrapper for working with genomic ranges in R
checks if region file is merged
Data frame to list conversion
outputs text if verbose flag is set
merge i.e. collapse overlpaping regions
Visualize regions or intervals
Download some useful datasets
bedr.join.multiple.region
join multiple region objects
checks if region file is sorted
join two region objects using a left outer join
sort a region file
checks if binary is in the path
bed dataframe to index string
verifies the reference sequence in a vcf
Get region size
process.input
split a vector of strings into tabular data
Initialize some config settings for bedr
convert bed to vcf
checks if regions in object a are found in object b
checks if regions in object a are found in object b
Gets the sort order of a region index similar to the order command
sort a region file
output R objects as tmpfiles
Determine input format
Get adjacent flanks from regions
subtracts features or ranges in object b from object a
permute a set of regions
gets the length of each chromosome for a species/build
return a set of regions for the examples and unit testing
write a vcf object
read a ucsc table into R
generates a set of random regions
Query fasta sequence
Main bedtools wrapper function.
calculate the jaccard distance between sets of intervals
Get adjacent flanks from regions
Compare sets of regions via jaccard and relative distance using permutation
convert a vcf to a bed file
Plot venn diagram
checks if region/index is valid
Interface to R's modifyList
Read a vcf into R
verifies that sequences are correct given coordinates and a reference
Calculate the relative distance between two sets of intervals
cluster intervals
convert object to bed format
convert a region index into a bed file dataframe
Main bedtools wrapper function.