3.4版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o参数“downloadFile”添加到fea_david()来选择是否将分析结果保存到当前目录o大卫现在需要https。这导致一些系统错误。(希望如此)的临时解决方案是在本地安装一些证书。看到RDAVIDWebService帮助:https://support.bioconductor.org/p/70090/ # 72226 3.2版本的变化- - - - - - - - - - - - - - - - - - - - - - - -新功能HTML装饰图案o由两部分构成的网络:节点现在圆形和方形(只用于“静态”情节)o PlotGoAncestors:添加参数nCharTerm o clustersDistance:添加参数“clustMethod”和“平均”设置为默认的聚类方法。o证据:添加参数fea_topGO(新数据对象:GOEvidenceCodes) o参数vExprColors functionalNetwork补充道。o顶点大小现在允许为每个基因设置一个值。修正o fea2incidMat:过滤负3.0版本的变化- - - - - - - - - - - - - - - - - - - - - - - -新特性图形用户界面(GUI) o新的有限元分析工具:topGO和计(GSEA) o情节基因表达(上/下)功能网络(因为重击。版本2.1)o plotGoAncestors plotKegg接口更改o函数重命名或替换:o toMatrix / adjMatrix: fea2incidMat o plotMetagroupsDistance: clusterDistance o query_gtLinker & getResults_gtLinker: fea_gtLinker & fea_gtLinker_getResults o query_david & getResults_david: fea_david & format_david o report_gtLinker & report_david: FGNet_report o intersectionNetwork:现在包括在functionalNetwork 2.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - -新特性在functionalNetwork o表达式:现在可以绘制基因表达(上/下)网络。o plotGoAncestors:新功能。o报告:添加选项只显示最具体的条款去(树叶:本体的底部)。 Kegg pathway plot can now be plotted and saved locally. o Added p-value stats to clusters matrix. o Side colors added to metagroups heatmap. o toMatrix: added argument sepChar, legendPrefix and filterOperator. Attribute and threshold renamed to filterAttribute and filterThreshold. o functionalNetwork: added arguments plotIntersectionNetwork,plotTitleSub. o getResults_gtLinker: added argument organism (adds the prefix to kegg id). o getResults_david: inputFileLocation renamed to fileName BUG FIXES o GO ontology plot: now done locally through plotGoAncestors. o toMatrix: Accepts characters in cluster column (provides more flexibility with non-clustered/modular FEA and support to build term-term and term-genes networks). Arguments: legendMg renamed to legendText. CHANGES IN VERSION 2.0 ------------------------ NEW FEATURES o The networks can now be plotted for terms in addition to genes. o In the report, clicking on the plots allows to see the plot at full size next to the terms table (if the screen resolution allows it). o ToMatrix(): Added arguments 'key' (to choose either genes or terms) and 'removeFiltered' terms. Renamed main argument (geneTermSets) to 'results'. o IntersectionNetwork() shows a warning if there is no intersection. Added argument 'plotAllMg' to allow choosing wether to plot unconnected metagroups or not. o FunctionalNetwork() changed the two main arguments to a single one, which is the raw output from toMatrix() (a list with names: c("metagroupsMatrix", "gtSetsMatrix", "filteredOut")). Added arguments: 'eColor' to provide the edges color, and 'weighted' to draw the edge width according to the number of shared gene-term sets. o Reports: Added argument 'downloadGOtree' to allow choosing wether to download the go term trees png (slower) or just provide the link to the web tool. BUG FIXES o functionalNetwork() now correctly writes either "cl" or "mg" in the legend. CHANGES IN VERSION 1.3.1 ------------------------ NEW FEATURES o adjMatrix() has been renamed to toMatrix() o GO png trees are now automatically downloaded when generating the report o functionalNetwork: metagroup/cluster legend order has been changed to alphabetical BUG FIXES o Minor bug fixes CHANGES IN VERSION 1.2 ------------------------ NEW FEATURES o Query David through web service (RDAVIDWebService): Avoids limitations of API interface o Added argument KeepColors to functionalNetwork and intersectionNetwork: Keeps the same color for each group even if some are filtered out. o Added argument geneLabels to getResults_david: Allows to replace the IDs for a gene name/symbol in the plots BUG FIXES o Minor bug fixes CHANGES IN VERSION 1.1.1 ------------------------ BUG FIXES o query_david: Checks whether the server accepted the query o MAN pages using query_david: Reduced yeast example to 15 genes. In windows, with the whole gene list, the server returns "Error: Expectation failed". CHANGES IN VERSION 1.0.0 ------------------------ NEW FEATURES o Package released