Integration of Interactive Genome Views with R

• Activity Number: 335
• Type: Topic Contributed
• Date/Time: Tuesday, August 2, 2011 : 10:30 AM to 12:20 PM
• Sponsor: Section on Statistical Graphics
• Author(s): Michael Lawrence*+ and Peter Danenberg and Robert Gentleman and Nicholas Lewin-Koh
• Companies: Genentech Research and Early Development and University of Southern California and Genentech Research and Early Development and Genentech Inc.
• Keywords: interactive graphics ; genome browser ; R

Abstract

We have integrated the R platform for statistical computing with IGB, a widely used genome browser written in Java. The goal is to leverage the synergy of the statistical functionality in R, including numerical algorithms and graphics, with the interactive, genome-oriented views provided by IGB. We will demonstrate the control of IGB from R, as well as the use of IGB plugins that, unbeknownst to the naive user, are implemented in R. IGB and R share data structures, without inefficient duplication. R plots, including those generated by the VisNAB package, are coordinated with IGB views. For example, selection in one results in a selection in another. The results of R-based analyses may be displayed in IGB, helping the user quickly locate the interesting parts of a genome-wide dataset. Interesting features discovered in IGB may be passed back to R for more focused analysis. We will provide an overview of these features and give a live demonstration of the software.