# #——knitrSetup,包括= FALSE ------------------------------------------------ 库(knitr) opts_chunk美元集(out.extra = '风格= "显示:块;保证金:汽车“fig.align =“中心”,fig.width = 12, fig.height = 12,整洁= TRUE) # #——风格,包括= FALSE,呼应= FALSE,结果= '飞机 '------------------------- BiocStyle:减价 () ## ---- installNetBoxr eval = FALSE ----------------------------------------------- # (“netboxr BiocManager:安装 ") ## ---- loadLibrary、消息= FALSE警告= FALSE -------------------------------- 库(netboxr) # #——searchHelp eval = FALSE,整洁= FALSE --------------------------------------- # 帮助(包= " netboxr ") ## ---- showHelp eval = FALSE,整洁= FALSE ----------------------------------------- # 帮助(geneConnector) # ? geneConnector # #——netboxrExampleNetwork ---------------------------------------------------- 数据(netbox2010) sifNetwork < - netbox2010美元网络graphReduced < - networkSimplify (sifNetwork导演= FALSE) # #——netboxrExampleGene ------------------------------------------------------- geneList < - as.character (netbox2010 geneList美元)长度(geneList) # #——netboxrExampleGeneConnector fig.width = 12,----------------- ##使用Benjamini-Hochberg方法对链接器候选项进行多个假设修正。##使用边间性方法检测网络中的社区结构。- geneConnector(geneList=geneList, networkGraph=graphReduced, directed=FALSE, pValueAdj="BH"， pValueCutoff=threshold, communityMethod="ebc"，#添加边缘注释库(RColorBrewer) edges <- results$netboxOutput interactionType<-unique(edges[，2]) interactionTypeColor<-brewer.pal(length(interactionType)，name="Spectral") edgeColors<-data.frame(interactionType,interactionTypeColor,stringsAsFactors =FALSE) colnames(edgeColors)<-c("INTERACTION_TYPE"，"COLOR") netboxGraphAnnotated <- annotateGraph(netboxResults = results, edgeColors = edgeColors, directed =FALSE，#检查所选连接器linkerDF <- results$neighborData linkerDF[linkerDF$pValueFDR . linkerDF]的p值 0.1) # #——sessionInfo -------------------------------------------------------------- sessionInfo ()