NEWS

GSRI 2.0.0

Complete rewrite, making the current GSRI package largely incompatible with any GSRI 1.*.* version
All results are now stored in an object of class 'Gsri' which is central for all the analysis in the package.
All user-relevant interfaces are now methods using the S4 class system.
The method 'gsri' is central for all analyses and includes capabilities of the deprecated 'gsriFromFile' and 'gsri' functions. The capability of the 'gsriFromFile' function in reading data files has been moved to the 'read*' methods. The capabilities for plotting, exporting to files etc. of the 'gsri' and 'gsriFromFile' functions has been moved to dedicated methods.
Bootstrapping of group labels has been replaced by bootstrapping expression intensities within groups.
The internal functionality of the 'GSRI' package has mainly been replaced by the 'les' package, including new features such as weighting.
Gene set can be defined using the classes of the 'GSEABase' package
Function for reading .gmt files has been dropped in favor of 'getGmt' of the 'GSEABase' package
Change of nearly all argument names