CHANGES IN VERSION 1.4.0 ------------------------ o [Bug Fix] - `findStudiesInCluster`: single-element clusters return the correct study now, instead of `null` o [Major] - `findStudiesInCluster`: the output includes PC number of the participating study in the cluster and the variance explained by them. With `studyTitle=FALSE`, the output will be a data frame, not a character vector. - `subsetEnrichedPathways`: the new argument `include_nes` is added. If it is set to `TRUE`, the output will include NES from GSEA. - `getRAVInfo` and `getStudyInfo`: two new functions to extract basic metadata for RAVs and studies, respectively. - We characterize RAVs that are harder to interpret with the currently available information associated with them (more detail can be found bit.ly/RAVmodel_characterization). For the following functions, any output including those RAVs will have a defulat message: `meshTable`, `drawWordcloud`, `heatmapTable`, `validatedSignatures`. You can snooze this by setting `filterMessage = FALSE` - New required parameter `RAVmodel` for the following functions: `annotatePC`,`heatmapTable` and `validatedSignatures`. - New accessor `version` is available to check the version of RAVmodel - New function `availableRAVmodel` will output the different versions of RAVmodels available for downloading now. - `getModel` function now takes a new argument, `version`, to specify the version of RAVmodel to download. o [Minor] - miniRAVmodel is updated CHANGES IN VERSION 1.2.0 ------------------------ o [Bug Fix] - `n` argument of `annotatePC` was hard-coded. Now it can return different number of enriched pathways. - `abs` argument of `annotatePC` was fixed. - Fix wrongfully assigned variable within `plotAnnotatedPCA` function. o [Major] - `drawWordcloud` has a new argument `droplist`. - Argument name for `plotAnnotatedPCA` is changed from `PCs` to `PCnum`. - New argument `studyTitle` for `findStudiesInCluster` function. o [Minor] - Description of the package is updated. - If non-existing index is provided for any function, it will return with the error message. CHANGES IN VERSION 1.0.0 ------------------------ o Initial release of the 'GenomicSuperSignature' package