bedr1.0.7 package

bed dataframe to index string

convert bed to vcf

A bedtools wrapper for working with genomic ranges in R

join multiple region objects

join two region objects using a left outer join

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

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 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

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

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

write a vcf object