NEWS

GenomicSuperSignature 1.4.0

[Bug Fix] - 'findStudiesInCluster': single-element clusters return the correct study now, instead of 'null'
[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.
[Minor] - miniRAVmodel is updated

[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.
[Major] - 'drawWordcloud' has a new argument 'droplist'. - Argument name for 'plotAnnotatedPCA' is changed from 'PCs' to 'PCnum'. - New argument 'studyTitle' for 'findStudiesInCluster' function.
[Minor] - Description of the package is updated. - If non-existing index is provided for any function, it will return with the error message.