# # # R代码从装饰图案的mirIntegrator来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:mirIntegrator。Rnw: 115 - 116 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # set.seed (42 l) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:mirIntegrator。Rnw: 120 - 126 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #要求(“mirIntegrator”)的数据(kegg_pathways)数据(mirTarBase) kegg_pathways < - kegg_pathways[18:20] #删除这个增加所有通路。augmented_pathways < - integrate_mir (kegg_pathways mirTarBase)头(augmented_pathways) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:mirIntegrator。Rnw: 138 - 139 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # augmented_pathways美元”路径:hsa04122“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:mirIntegrator。Rnw: 157 - 161 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据(names_pathways) plot_augmented_pathway (kegg_pathways“路径:hsa04122”美元,美元augmented_pathways“路径:hsa04122 names_pathways["路径:hsa04122 "]) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:mirIntegrator。Rnw: 167 - 170 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plot_augmented_pathway (kegg_pathways“路径:hsa04122”美元,美元augmented_pathways“路径:hsa04122 names_pathways["路径:hsa04122 "]) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:mirIntegrator。Rnw: 189 - 193 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (augmented_pathways)数据(kegg_pathways)数据(names_pathways) plot_change (kegg_pathways、augmented_pathways names_pathways) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:mirIntegrator。Rnw: 198 - 199 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plot_change (kegg_pathways、augmented_pathways names_pathways, sizeT = 10) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:mirIntegrator。Rnw: 209 - 214 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (augmented_pathways)数据(kegg_pathways)数据(names_pathways) pathways2pdf (kegg_pathways [18:20], augmented_pathways [18:20], names_pathways [18:20],“three_pathways.pdf”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:mirIntegrator。Rnw: 238 - 240 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (GSE43592_miRNA)数据(GSE43592_mRNA) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:mirIntegrator。Rnw: 254 - 285 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #要求(图)要求(ROntoTools)数据(GSE43592_mRNA)数据(GSE43592_miRNA)数据(augmented_pathways)数据(names_pathways) lfoldChangeMRNA < - GSE43592_mRNA logFC名称(lfoldChangeMRNA) < - GSE43592_mRNA美元entrez lfoldChangeMiRNA < - GSE43592_miRNA logFC名称(lfoldChangeMiRNA) < - GSE43592_miRNA美元entrez keggGenes < -独特(unlist(拉普兰人(augmented_pathways、节点)))interGMi < -相交(keggGenes, GSE43592_miRNA entrez美元)interGM <——相交(keggGenes, GSE43592_mRNA entrez美元)# #进行实际分析,nboot应该> = 2000佩雷斯< - pe (x = c (lfoldChangeMRNA lfoldChangeMiRNA),图= augmented_pathways nboot = 200, verbose = FALSE)消息(粘贴(“有”,长度(独特(GSE43592_miRNA entrez美元)),“microrna meassured和长度(interGMi),包含在分析。”))消息(粘贴(“有”,长度(独特(GSE43592_mRNA entrez美元)),“mrna meassured和长度(interGM),包含在分析。”))夏(佩雷斯)rankList < < -总结- data.frame(夏,path.id = row.names(夏))tableKnames < - data.frame (path.id =名字(names_pathways) names_pathways) rankList < - (tableKnames, rankList合并。x =“路径。id”。y = "path.id") rankList <- rankList[with(rankList, order(pAcc.fdr)), ] head(rankList)