### R code from vignette source 'mirIntegrator.Rnw' ################################################### ### code chunk number 1: mirIntegrator.Rnw:115-116 ################################################### set.seed(42L) ################################################### ### code chunk number 2: mirIntegrator.Rnw:120-126 ################################################### require("mirIntegrator") data(kegg_pathways) data(mirTarBase) kegg_pathways <- kegg_pathways[18:20] #delete this for augmenting all pathways. augmented_pathways <- integrate_mir(kegg_pathways, mirTarBase) head(augmented_pathways) ################################################### ### code chunk number 3: mirIntegrator.Rnw:138-139 ################################################### augmented_pathways$"path:hsa04122" ################################################### ### code chunk number 4: mirIntegrator.Rnw:157-161 ################################################### data(names_pathways) plot_augmented_pathway(kegg_pathways$"path:hsa04122", augmented_pathways$"path:hsa04122", names_pathways["path:hsa04122"] ) ################################################### ### code chunk number 5: mirIntegrator.Rnw:167-170 ################################################### plot_augmented_pathway(kegg_pathways$"path:hsa04122", augmented_pathways$"path:hsa04122", names_pathways["path:hsa04122"] ) ################################################### ### code chunk number 6: mirIntegrator.Rnw:189-193 ################################################### data(augmented_pathways) data(kegg_pathways) data(names_pathways) plot_change(kegg_pathways,augmented_pathways, names_pathways) ################################################### ### code chunk number 7: mirIntegrator.Rnw:198-199 ################################################### plot_change(kegg_pathways,augmented_pathways, names_pathways, sizeT = 10) ################################################### ### code chunk number 8: mirIntegrator.Rnw:209-214 ################################################### data(augmented_pathways) data(kegg_pathways) data(names_pathways) pathways2pdf(kegg_pathways[18:20],augmented_pathways[18:20], names_pathways[18:20], "three_pathways.pdf") ################################################### ### code chunk number 9: mirIntegrator.Rnw:238-240 ################################################### data(GSE43592_miRNA) data(GSE43592_mRNA) ################################################### ### code chunk number 10: mirIntegrator.Rnw:254-285 ################################################### require(graph) require(ROntoTools) data(GSE43592_mRNA) data(GSE43592_miRNA) data(augmented_pathways) data(names_pathways) lfoldChangeMRNA <- GSE43592_mRNA$logFC names(lfoldChangeMRNA) <- GSE43592_mRNA$entrez lfoldChangeMiRNA <- GSE43592_miRNA$logFC names(lfoldChangeMiRNA) <- GSE43592_miRNA$entrez keggGenes <- unique(unlist( lapply(augmented_pathways,nodes) ) ) interGMi <- intersect(keggGenes, GSE43592_miRNA$entrez) interGM <- intersect(keggGenes, GSE43592_mRNA$entrez) ## For real-world analysis, nboot should be >= 2000 peRes <- pe(x= c(lfoldChangeMRNA, lfoldChangeMiRNA ), graphs=augmented_pathways, nboot = 200, verbose = FALSE) message(paste("There are ", length(unique(GSE43592_miRNA$entrez)), "miRNAs meassured and",length(interGMi), "of them were included in the analysis.")) message(paste("There are ", length(unique(GSE43592_mRNA$entrez)), "mRNAs meassured and", length(interGM), "of them were included in the analysis.")) summ <- Summary(peRes) rankList <- data.frame(summ,path.id = row.names(summ)) tableKnames <- data.frame(path.id = names(names_pathways),names_pathways) rankList <- merge(tableKnames, rankList, by.x = "path.id", by.y = "path.id") rankList <- rankList[with(rankList, order(pAcc.fdr)), ] head(rankList)