## ----echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE--------------------- library(ELMER.data) library(ELMER) library(DT) library(dplyr) library(BiocStyle) ## ----eval=TRUE,fig.cap=" TF ranking plot: For a given enriched motif, all human TF are ranked by the statistical $-log_{10}(P-value)$ assessing the anti-correlation level of candidate Master Regulator TF expression with average DNA methylation level for sites with the given motif. As a result, the most anti-correlated TFs will be ranked in the first positions. By default, the top 3 most anti-correlated TFs, and all TF classified by TFClass database in the same family and subfamily are highlighted with colors blue, red and orange, respectively."---- load("result/getTF.hypo.TFs.with.motif.pvalue.rda") motif <- colnames(TF.meth.cor)[1] TF.rank.plot( motif.pvalue = TF.meth.cor, motif = motif, save = FALSE )