## ----Summary of the community enrichment", class.output="scroll-200"---- GRN = plotCommunitiesEnrichment(GRN, plotAsPDF = FALSE, pages = c(5)) ## ----TFEnrichmentCal, echo=FALSE, eval = FALSE, class.output="scroll-200"----- # GRN = calculateTFEnrichment(GRN, ontology = "GO_BP") ## ----TFEnrichment, echo=TRUE, fig.cap="Enrichment summary for EGR1.0.A", fig.height=7, fig.width = 12, class.output="scroll-200"---- GRN = plotTFEnrichment(GRN, plotAsPDF = FALSE, n = 3, pages = c(1)) ## ----TFEnrichment2, echo=TRUE, fig.cap="Enrichment summary for selected TFs and the whole eGRN network", fig.height=7, fig.width = 15, class.output="scroll-200"---- GRN = plotTFEnrichment(GRN, plotAsPDF = FALSE, n = 3, pages = c(5)) ## ----saveObject3, echo=TRUE, include=TRUE, eval=FALSE, class.output="scroll-200"---- # GRN = deleteIntermediateData(GRN) # saveRDS(GRN, GRN_file_outputRDS) ## ---- class.output="scroll-200"----------------------------------------------- sessionInfo()