This is a tutorial module for writing GenePattern modules in R. It contains a very simple module that accepts a GCT as input and increments it based on an input value, writing the resulting matrix to a new output GCT. While this is not by itself a very interesting module, it illustrates some basic techniques useful to an R developer trying to get started with GenePattern.
A new developer should have a look at the R code, the r.package.info file, and the manifest to get started. The first two are most specific to R development and will be the most immediately useful. While the manifest is a fairly typical example for any GenePattern module, it's the bridge from GenePattern to the R code and sets up the interface between the two. All three files are heavily annotated so that information will not be repeated here.
The Developers Crash Guide contains some of my tips, tricks, and pitfalls for developing GenePattern modules in R. Like the Packages guide, I considered these somewhat too detailed to include in the Programmers Guide.
The Mac platform guide contains detailed info for working with R in GenePattern on Mac OS X as there are special challenges for this platform. A good deal of this information is in our Administrators Guide but is more up-to-date. There is some repetition between the two guides but also not complete overlap; the intention is to eventually merge and rectify the two documents. For now, it's important to at least have the info available in some form.
The Configuration guide contains some information on configuring R for GenePattern. Again, most if not all of this information will end up in the Administrators Guide eventually.