bedr1.1.5 package

merge i.e. collapse overlpaping regions

Visualize regions or intervals

Main bedtools wrapper function.

Initialize some config settings for bedr

sort a region file

sort a region file

subtracts features or ranges in object b from object a

outputs text if verbose flag is set

checks if binary is in the path

cluster intervals

convert object to bed format

output R objects as tmpfiles

Determine input format

Data frame to list conversion

Download some useful datasets

Get adjacent flanks from regions

get BEDPE ID from VCF ID

gets the length of each chromosome for a species/build

return a set of regions for the examples and unit testing

Query fasta sequence

generates a set of random regions

get BEDPE ID from VCF ID

Get adjacent flanks from regions

checks if regions in object a are found in object b

checks if regions in object a are found in object b

convert a region index into a bed file dataframe

checks if region file is merged

checks if region file is sorted

permute a set of regions

process.input

read a ucsc table into R

Read a vcf into R

Calculate the relative distance between two sets of intervals

Get region size

split a vector of strings into tabular data

Main bedtools wrapper function.

Plot venn diagram

Compare sets of regions via jaccard and relative distance using permut...

convert a vcf to a bed file

convert a vcf to a bedpe file

write a vcf object

adjust coordinates for a BEDPE file

bed dataframe to index string

convert bed to vcf

join multiple region objects

join two region objects using a left outer join

verifies the reference sequence in a vcf

checks if region/index is valid

verifies that sequences are correct given coordinates and a reference

calculate the jaccard distance between sets of intervals

Interface to R's modifyList

Gets the sort order of a region index similar to the order command