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### R code from vignette source 'mirIntegrator.Rnw'
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### code chunk number 1: mirIntegrator.Rnw:115-116
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set.seed(42L)
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### code chunk number 2: mirIntegrator.Rnw:120-126
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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)
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### code chunk number 3: mirIntegrator.Rnw:138-139
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augmented_pathways$"path:hsa04122"
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### code chunk number 4: mirIntegrator.Rnw:157-161
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data(names_pathways)
plot_augmented_pathway(kegg_pathways$"path:hsa04122",
augmented_pathways$"path:hsa04122",
names_pathways["path:hsa04122"] )
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### code chunk number 5: mirIntegrator.Rnw:167-170
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plot_augmented_pathway(kegg_pathways$"path:hsa04122",
augmented_pathways$"path:hsa04122",
names_pathways["path:hsa04122"] )
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### code chunk number 6: mirIntegrator.Rnw:189-193
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data(augmented_pathways)
data(kegg_pathways)
data(names_pathways)
plot_change(kegg_pathways,augmented_pathways, names_pathways)
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### code chunk number 7: mirIntegrator.Rnw:198-199
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plot_change(kegg_pathways,augmented_pathways, names_pathways, sizeT = 10)
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### code chunk number 8: mirIntegrator.Rnw:209-214
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data(augmented_pathways)
data(kegg_pathways)
data(names_pathways)
pathways2pdf(kegg_pathways[18:20],augmented_pathways[18:20],
names_pathways[18:20], "three_pathways.pdf")
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### code chunk number 9: mirIntegrator.Rnw:238-240
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data(GSE43592_miRNA)
data(GSE43592_mRNA)
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### code chunk number 10: mirIntegrator.Rnw:254-285
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require(graph)
require(ROntoTools)
data(GSE43592_mRNA)
data(GSE43592_miRNA)
data(augmented_pathways)
data(names_pathways)
lfoldChangeMRNA <- GSE43592_mRNA$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)
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