Using BED files with epiviz

18.12.2014 in epivizr using tags epivizr

On a twitter exchange I showed A. Quinlan how to use epivizr to load data from a custom bed file. Here is the code I gave him:


# download example bed file
download.file("", destfile="test.bed.gz", method="curl")

# start UI
mgr <- startEpiviz(workspace="mi9NojjqT1l")

# import bed file
gr <- import(BEDFile("test.bed.gz"))

# drop data from unplaced contigs
gr <- keepSeqlevels(gr, paste0("chr",c(1:22,"X","Y")))

# add track with bed file data
dev <- mgr$addDevice(gr, "example bed")

# finish up

Also at

The idea behind the epivizr BioC package is that it can use that infrastructure to import a lot of data formats into GenomicRanges-like objects one can manipulate (say, filter or transform), and have interactive visualization that reflects those manipulations immediately. However, it’s a little cumbersome for the use-case of where you have data on a BED file that you don’t need to manipulate, but just explore visually.

An option we’d like to get started with to support this contextual-data use-case is to write small programs that would use, say bedtools for example, to implement the epiviz Data Provider API and serve data directly from a bed file.