## ----eval=TRUE, message=FALSE, warning = FALSE, results = "hide"--------- # Load results from previous sections mae <- get(load("mae.rda")) load("result/getMotif.hypo.enriched.motifs.rda") ## ----eval=TRUE, message=FALSE, warning = FALSE, results = "hide"--------- ## identify regulatory TF for the enriched motifs TF <- get.TFs(data = mae, group.col = "definition", group1 = "Primary solid Tumor", group2 = "Solid Tissue Normal", mode = "unsupervised", enriched.motif = enriched.motif, dir.out = "result", cores = 1, label = "hypo") ## ----eval=TRUE, message=FALSE, warning = FALSE--------------------------- # get.TFs automatically save output files. # getTF.hypo.TFs.with.motif.pvalue.rda contains statistics for all TF with average # DNA methylation at sites with the enriched motif. # getTF.hypo.significant.TFs.with.motif.summary.csv contains only the significant probes. dir(path = "result", pattern = "getTF") # TF ranking plot based on statistics will be automatically generated. dir(path = "result/TFrankPlot/", pattern = "pdf")