CHANGES IN VERSION 1.5.5 ------------------------ o The default selection of the measure to use for ROC and FP curves have been changed to improve consistency. Now, the preferred order is pval, padj, score. The behaviour of previous versions can be obtained by setting prefer_pval = FALSE in calculate_performance(). Note that the type of measure that is used to calculate a certain performance value can be retrieved from the respective slots of the COBRAPerformance and COBRAPlot objects. o Improved robustness in selection of measure to use for FDR/TPR and FDR/NBR curves, especially for methods where both p-values and scores are available. o Additional validity checks for pval and padj slots CHANGES IN VERSION 1.5.1 ------------------------ o Added support for false sign rate calculations CHANGES IN VERSION 0.99.10 -------------------------- o Fixed the call to plot_upset to avoid duplicate definition of arguments CHANGES IN VERSION 0.99.9 ------------------------- o Added CITATION file, extended some examples CHANGES IN VERSION 0.99.8 ------------------------- o Include UpSet plots (Lex et al, IEEE Transactions on Visualization and Computer Graphics 2014) CHANGES IN VERSION 0.99.7 ------------------------- o Allow linewidth to be set, add Venn diagrams based on rank cutoffs CHANGES IN VERSION 0.99.5 ------------------------- o Updated documentation CHANGES IN VERSION 0.99.4 ------------------------- o Expanded tests, added experimental function to reorder factor levels before plotting CHANGES IN VERSION 0.99.3 ------------------------- o Bug fixes CHANGES IN VERSION 0.99.2 ------------------------- o Fixed replacement methods for COBRAPlot class CHANGES IN VERSION 0.99.1 ------------------------- o Removed benchmarkR dependence CHANGES IN VERSION 0.3.13 ------------------------- o Adapted package for Bioconductor submission CHANGES IN VERSION 0.3.11 ------------------------- o Renamed to iCOBRA CHANGES IN VERSION 0.3.9 ------------------------ o Improved constructors CHANGES IN VERSION 0.3.8 ------------------------ o Added check for duplicated feature IDs CHANGES IN VERSION 0.3.7 ------------------------ o Fixed bug causing problems for Venn diagrams if only one method is available o Included information texts in app CHANGES IN VERSION 0.3.5 ------------------------ o Simplified constructors CHANGES IN VERSION 0.3.4 ------------------------ o Modified calculation of overlaps CHANGES IN VERSION 0.3.2 ------------------------ o Added unit tests CHANGES IN VERSION 0.3.1 ------------------------ o Updated information messages in app CHANGES IN VERSION 0.3.0 ------------------------ o Bug fixes in app o Addition of small example data set o Addition of information banners to app CHANGES IN VERSION 0.2.0 ------------------------ o Added deviation plot o Bug fixes