# #——knitrSetup,包括= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(knitr)美元opts_chunk组(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= '网络”- - - - - - - - - - - - - - - - - - - - - - - - - BiocStyle::减价()# #——installNetBoxr, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # BiocManager::安装(“netboxr”) # #——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, fig.height = 12 - - - - - - - - - - - - - - - - - - # #使用Benjamini-Hochberg方法做多个假设# #修正链接器的候选人。# #使用edge-betweeness方法检测网络中的社区结构。阈值< - 0.05结果< geneConnector (geneList = geneList networkGraph = graphReduced = FALSE, pValueAdj =“黑洞”,pValueCutoff =阈值,communityMethod =“ebc keepIsolatedNodes = FALSE) #添加边注释库(RColorBrewer) < -边缘结果美元netboxOutput interactionType <独特(边缘[2])interactionTypeColor < -brewer.pal(长度(interactionType)、name =“光谱”)edgeColors < -data.frame (interactionType、interactionTypeColor stringsAsFactors = FALSE) colnames (edgeColors) < - c (“INTERACTION_TYPE”、“颜色”)netboxGraphAnnotated < - annotateGraph (netboxResults =结果,edgeColors = edgeColors = FALSE,链接器= TRUE) #检查选中的链接器linkerDF < -结果的假定值美元neighborData linkerDF [linkerDF pValueFDR美元 0.1)# #——sessionInfo - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sessionInfo ()