Changes in version 1.10.2: o BUGFIX: The wiki2cmap function now excludes empty files downloaded from wikipathways from parsing instead of throwing an error. o BUGFIX: The reactom2cmap function is currently defunct, because the reactome.db package is broken. o BUGFIX: Added missing export for go2cmap function. Changes in version 1.10.1: o BUGFIX: Fixed the romer_score method to accomodate the change in argument order in limma's romer function. Changes in version 1.10.0: o CHANGE: Version bump for BioC update. Changes in version 1.9.2: o BUGFIX: Updated geneIndex method to accept both symbols2indices and id2indices functions from limma, depending on the limma version. Changes in version 1.8.1: o BUGFIX: Updated extraction of big.max objects while maintaining row.names. Changes in version 1.7.2: o CHANGE: Helper functions KEGG2cmap, reactome2cmap, wiki2cmap and go2cmap have two additional parameters, min.size and max.size, restricting the output to gene sets containing members within the specified range. o CHANGE: Method camera_score now outputs correlations in column 'effect'. o BUGFIX: Correct numbers of annotated genes are now returned for each set. Changes in version 1.7.1: o CHANGE: Vignettes are now stored in vignettes directory. Changes in version 1.5.4: o NEW: The bigmemory and bigmemoryExtras packages are not optional, enabling use of gCMAP on Windows Changes in version 1.5.3: o NEW: Updated titles of vignettes Changes in version 1.5.2: o BUGFIX: Updated eSet construction in mapNmerge function Changes in version 1.5.1: o BUGFIX: fixed incorrect varMetaData element definition in .process_counts Changes in version 1.3.5: o NEW: DESeq package is now listed as 'Suggested' instead of 'Depends' Changes in version 1.3.4: o NEW: Removed lattice and reshape dependencies. o NEW: Removed cmapQAPlot function. o NEW: Added generate_gCMAP_NChannelSet's 'report.center' parameter. Changes in version 1.3.3: o NEW: Experimented with cmapQAPlot function (removed again in version 1.3.4). Changes in version 1.3.2: o NEW: mgsa_score method wrapping the model-based gene set analysis approach available in the mgsa package. Changes in version 1.3.1: o NEW: KEGG2cmap, reactome2cmap, wiki2cmap and go2cmap to functions to generate CMAPCollections from public annotation databases o NEW: upIds and downIds methods for CMAPCollection objects. Changes in version 1.3.0: o NEW: fisher_score method now accepts NChannelSets as 'sets' and thresholds a channel of choice on the fly. o BUGFIX: induceCMAPCollection method was updated to fix a bug that prevented processing of certain single-sample eSets. o NEW: parameters 'center.z' and 'center.log_fc' for the generate_gCMAP_NChannelSet function, centering each column of the score matrix on the column mean, median or density peak. (Internally, the NEW: 'center_eSet' function is called.) o NEW: function 'center_eSet' to center columns of eSet channels on either their kernel density peak, their mean or their median. o NEW: function mergeCMAPs to combined two eSets that share class, varLabels, annotation and assayDataElementNames. o BUGFIX: Fixed missing gene names in featureScores method with CMAPCollections queries containing single-gene sets. o NEW: splitPerturbations function to split ExpressionSet (e.g. downloaded from ArrayExpress) by annotations provided in the phenoData slot. o NEW: eset_instances function to generate lists eSets from larger datasets by specifying an instance.matrix. o NEW: setSizes methods for CMAPCollections returns a data.frame with the number of members for each gene set stored in the Collection. o NEW: fisher_score method now reports z-scores in the effect column instead of log-odds-ratio. The latter are returned in the NEW: , separate LOR column. o NEW: featureScores method now return list of matched identfiers when dispatched on two CMAPCollection. o NEW: Added 'density.only', 'level.only' and 'strip.only' parameters to the CMAPResults plot method to selectively return only one plot component. o IMPROVED Reduced memory footprint of gsealm_jg_score and induceCMAPCollection methods. o CHANGED: By default, 'removeShift' option for gsealm_jg_score and gsealm_score methods is now set to FALSE. o BUGFIX: Corrected sign of effect size for fisher_score for perfect overlap between set and query. o IMPROVED: Improved plot method for CMAPResults objects, lattice package is no longer required. Changes in version 1.1.4: o BUGFIX: The gealm_score method is not defined for queries with missing values and will now return the corresponding error message. o BUGFIX: GeneSetCollections containing only one set are processed correctly by gsealm_score. Changes in version 1.1.3: o BUGFIX: Corrected sign of effect size for fisher_score for perfect overlap between set and query. Changes in version 1.1.2: o BUGFIX: Fixed log-odds calculation in fisher_score: non-overlapping sets now get a log odds ratio of 0 Changes in version 1.1.1: o IMPROVED: Reduced memory footprint of induceCMAPCollection method for bigmemory-backed eSet objects. Changes in version 1.1.0: o NEW: Version number was increased for the Bioconductor release. Changes in version 0.99.6: o IMPROVED: Updated mapIdentifiers method for SignedGeneSet class now handles more different annotation types. Changes in version 0.99.5: o NEW: The BigMatrix package changed its name to bigmemoryExtras. Currently, bigmemoryExtras only supports Mac and Unix platforms, thus gCMAP does not support Windows, either. Changes in version 0.99.1: o NEW: First release of the gCMAP package to Bioconductor.