1 Overview

The igvR package provides easy programmatic access in R to the web-based javascript library igv.js. R’s access to data, and operations upon data, are complemented by igv’s richly interactive web browser interface to display and explore genomic and epigentic data.

In this vignette we present a somewhat contrived ChIP-seq study - contrived in that it is not organized around an actual research problem. Instead, this vignette demonstrates methods you would likely use to do visual QC and exploratory data analysis a ChIP-seq experiment.

We begin with ENCODE data of CTCF binding on chromosome 3, on the hg19 reference genome, in the vicinity of the GATA2 gene. We will

The two images below illustrate the final state of igv in your browser at the conclusion of the code found below. The first view spans 35kb:

The second spans less than 1200 bases.