1.4.1版的更改:修正了NEWS的格式。Rd，在伙伴包gCMAPWeb中添加了附加小插图的参考。版本1.3.5:o NEW: DESeq包的更改现在被列为“建议”，而不是“依赖”。版本1.3.4:o NEW:删除晶格和重塑依赖。o新:删除cmapQAPlot功能。o新:添加generate_gCMAP_NChannelSet的'报告。中心的参数。o NEW:尝试了cmapQAPlot函数(在1.3.4版本中再次删除)。新版:新的mgsa_score方法包装了mgsa包中可用的基于模型的基因集分析方法。1.3.1版更改:o NEW:新增KEGG2cmap、reactome2cmap、wiki2cmap和go2cmap，用于从公共注释数据库生成CMAPCollection。o NEW:新增CMAPCollection对象的upIds和downIds方法。version 1.3.0: o NEW: fish_score方法现在接受NChannelSets作为'sets'，并在运行中阈值一个选择的通道。o bug修复:induceCMAPCollection方法更新以修复阻止处理某些单样本eSets的错误。 o NEW: 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: New function 'center_eSet' to center columns of eSet channels on either their kernel density peak, their mean or their median. o NEW: 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: New splitPerturbations function to split ExpressionSet (e.g. downloaded from ArrayExpress) by annotations provided in the phenoData slot. o NEW: New eset_instances function to generate lists eSets from larger datasets by specifying an instance.matrix. o NEW: 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. \itmeBUGFIX: 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.