CHANGES IN VERSION 1.16.0 ------------------------- NEW FEATURES o cn2lr now has methods for vector, matrix, and DataFrame (of Rle) and allows you to center your log2ratio values on 2 copies, or on a specified 'ploidy' for your sample. DEPRECATED AND DEFUNCT o The BAFSet and CNSet classes have moved from deprecated to defunct. These classes only added getter/setter methods for baf/lrr/cn. Since these only cover some possible assayDataElements, it is better to use x[i,j,k], where k is the name of an assayDataElement. o All RangedData-related things have now progressed to defunct. Please use GRanges for locData and everywhere else. Since the genoset package provides a common API for GenoSet, GRanges, and RangedData, I hope this will be a simple change for everyone. o sampleNames and featureNames are now *un-deprecated*. Feel free to use them. They just call colnames and rownames, respectively. I have defined my own rownames and colnames functions. The eSet ones seem to do a lot of extra work, and the getter versions read from the first assayDataElement, rather than pData and fData. I changed to the latter, so BigMatrix assayDataElements will remain untouched until you really mean to access them.