The Gaggle Vignette

These web pages accompany the vignette published with the Gaggle package. It explains how to use the Gaggle in conjunction with R. Before you begin, be sure you understand these concepts:
  • The Gaggle permits users to broadcast four kinds of data from program to program.
  • You must start the Gaggle Boss first -- this provides the 'backbone' over which the broadcasts take palce.
  • Every goose (i.e., any program adapted to the Gaggle) registers with the Boss when it starts up.
  • Most geese, and the Boss, are started vai Java Web Start -- just click on a link, the program is downloaded to your computer, and starts up. We provide these links in the web pages of this vignette.
  • The R Gaggle package is installed and loaded in the usual R manner.
The vignette comes in three parts:
  1. A simple introduction, using only R and Cytoscape, with a few simple broadcasts back and forth.

  2. We add the STRING goose, for discovering protein-protein interactions for a few human genes.

  3. We add a Name Translator goose, to translate STRING's cryptic protein names into GeneID's, as we broadcast the interactions back to R.