CHANGES IN VERSION 1.8.0 ------------------------- o Extended support for benchmarking user-defined inputs: - mixing of pre-defined and user-defined enrichment methods (functions `runEA` and `evalTypeIError`) - simplified passing on of additional arguments to user-defined enrichment methods for functions `runEA` and `evalTypeIError` o The TCGA RNA-seq compendium can now also be obtained via curatedTCGAData using `loadEData("tcga", mode = "cTD")` CHANGES IN VERSION 1.6.0 ------------------------- o New function `evalTypeIError`: type I error evalution by sample permutation - evaluation of >= 1 enrichment methods on >= 1 expression datasets - support for splitting permutations into blocks of defined size + invoking parallel evaluation of the partitions o New function `evalRandomGS` for evaluation of random gene sets: - estimates proportion of rejected null hypotheses (= fraction of significant gene sets) of an enrichment method when applied to random gene sets of defined size - evaluation of >= 1 enrichment methods on an expression dataset of choice o New argument `method` to the `evalRelevance` function for the evaluation of phenotype relevance of gene set rankings, choices include: - "wsum": computes a weighted sum of the relevance scores (default), - "auc": performs a ROC/AUC analysis based on the ROCR package, - "cor": computes a standard correlation such as Spearman's rank correlation, - a user-defined function for customized behaviors. o New function `metaFC` for summarizing fold changes of individual datasets across a compendium of expression datasets o New functions `plotDEDistribution` and `plotNrSamples` for exploring differential expression and sample size across a compendium of expression datasets o Extended support for user-defined benchmarking inputs including simplified plug-in of user-defined enrichment methods (thanks to Marcel Ramos @LiNk-NY)