EGSEA 1.1.1(2016-05-10) - - - - - - - - - - - - - - - - - - - - - - - - -改善:topSets(…)和“报告”的功能参数的EGSEA(…)功能。-改善:冗长和“打印。基地”可用性在egsea ()。现在可以导出单个方法的统计数据的输出egsea当打印。基础= TRUE。——补充道:弗莱(…)基因从limma设置测试包。——补充道:多种方法结合多种方法的假定值。看到egsea.combine ()。——固定:各种小虫子。EGSEA 1.1.4(2016-05-23) - - - - - - - - - - - - - - - - - - - - - - - - -改善:奥拉适应截止阈值logFC = 0如果没有德基因被发现在logFC = 1。在这两种情况下,截止阀值的调整假定值= 0.05。-改善:包的鲁棒性和允许单一使用EGSEA GSE分析来进行。 - Added: Ensemble mode is disabled if one base GSE method is provided. - Added: S4 class for the egsea() output, named EGSEAResults. - Added: generic methods: show(), summary(), plotHeatmap(), plotPathway(), plotMDS(), and plotSummary(). EGSEA 1.1.5 (2016-05-27) ------------------------ - Fixed: a minor bug in EGSEAResults when symbolsMap = NULL - Added: NA Gene Symbols are replaced with Feature IDs in the symbolsMap - Added: FRY to egsea.base() - Added: several sanity checks on the input parameters EGSEA 1.1.6 (2016-05-31) ------------------------ - Fixed: a minor bug in the calculation of the comparative analysis p-value. EGSEA 1.1.7 (2016-06-30) ------------------------ - Improved: the documentation of the methods in the vignette - Improved: the interpretation of the results in the vignette - Improved: the ranking when ties occur - Added: useDingbats = FALSE to pdf() when generating summary plots - Added: S4 class named GSCollectionIndex to store indexed gene set collections - Added: showSetByName() and showSetByID() to EGSEAResults and GSCollectionIndex - Added: plotGOGraph() to EGSEAResults - Updated: the GO graphs page of the comparative analysis - Added: GO graphs to the GO collection of the GeneSetDB - Fixed: minor bugs EGSEA 1.1.8 (2016-07-12) ------------------------ - Removed: EGSEAResults of IL13 from EGSEA and moved it to EGSEAdata - Updated: EGSEAdata object names in idxAnno EGSEA 1.1.9 (2016-08-19) ------------------------ - Fixed: a bug in buildIdx of mouse H gene set EGSEA 1.1.10 (2016-) ------------------------ - Added: two slots to the GSCollectionIndex: version and date - Added: citations of the base methods to the documentation of egsea.base() - Removed: rdata.dir from buildIdx functions - Added: the gene set collection version/update date to the GSCollectionIndex class - Added: an argument to egsea() and egsea.cnt() to return the analysis of limma results, which is keep.imma - Added: an argument to egsea() and egsea.cnt() to return the set scores of ssgsea, keep.set.scores - Added: a slot to the EGSEAResults, which is limmaResults - Added: a slot to the EGSEAResults, baseInfo - Added: limmaTopTable, getlimmaResults and getSetScores to the class EGSEAResults - Added: plotSummaryHeatmap to the class EGSEAResults - Improved: documentation across several functions.