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Sun, 03 Feb 2008
VanillaICE
Made a number of changes to the VanillaICE infrastructure. The main idea was to move away from storing SNP-level data and results from the HMM in the same R object. Classes HmmSnpSet, HmmSnpCopyNumberSet, and HmmSnpCallSet are defunct. Instead, we define a parameter class for the HMM -- HmmParameter -- and a class for storing the results from the HMM -- HmmPredict. The .Rd files were removed and rewritten. plotSnp methods were also modified to accomodate the changes in the class structure. In addition, a vignette was added to describe how one may create an instance of oligoSnpSet from BeadStudio processed data. The vignette VanillaICE.Rnw was rewritten. The example data, chromosome1, was changed to an oligoSnpSet.