bedscout

The goal of bedscout is to agglutinate relevant helper functions for useful comparisons we make between BED files using available libraries such as GenomicRanges and rtracklayer. The intention is not to replace their functionality or reinvent the wheel, but simplify the use of otherwise more complex and generic functions.

In the future I will also include here some visualization and simple statistics.

Installation

You can install the development version of bedscout from GitHub with:

# install.packages("devtools")
devtools::install_github("cnluzon/bedscout")

Example

This is a basic example which calculates the total overlap in basepairs between two GenomicRanges objects:

library(bedscout)
library(GenomicRanges)

gr_1 <- GRanges(seqnames = c("chr1"), IRanges(10, 20), strand = "-")
gr_2 <- GRanges(seqnames = c("chr1"), IRanges(15, 25), strand = "+")

total_bp_overlap(gr_1, gr_2, ignore.strand = TRUE)
#> [1] 6