CHANGES IN VERSION 1.3.7 ------------------------- o DaMiRseq performs multi-class classification anlysis. o The Stacking meta-learner can be composed by the user, setting the new parameter 'cl_type' of the DaMiR.EnsembleLearning() function. Any combination of the 8 classifiers is now allowed. o If the dataset is imbalanced, a 'Down-Sampling' strategy is automatically applied. o The DaMiR.FSelect() function has the new argument, called 'nPlsIter', which allows the user to have a more robust features set. In fact, several feature sets are generated by the bve_pls() fuction (embedded in DaMiR.FSelect()), setting 'nPLSIter' parameter greater than 1. Finally, an intersection among all the feature sets is performed to return those features which constantly occur in all runs. However, by default, 'nPlsIter = 1'. o DaMiR.Allplot() accepts also 'matrix' objects as well as NA values (which are not plotted). o The DaMiR.normalization() function estimates the dispersion, through the parameter 'nFitType'; as in DESeq2 package, the argument can be 'parametric' (default), 'local' and 'mean'. o In the DaMiR.normalization() function, the gene filtering is desabled if 'minCount = 0'. o In the DaMiR.EnsembleLearning() function, the method for implementing the Logistic Regression has been changed to allow multi-class comparisons; instead of the native 'lm' function, 'bayesglm' method implemented in the caret 'train' function, properly set, is now used. o The new parameter 'second.var' of the DaMiR.SV() function, allows the user to take into account a secondary variable of interest (factorial or numerical) that the user does not wish to correct for, during the sv identification.