## ----echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE--------------------- library(ELMER.data) library(ELMER) library(DT) library(dplyr) library(BiocStyle) ## ----eval=TRUE, message=FALSE, warning = FALSE,results = "hide"--------------- # Load results from previous sections mae <- get(load("mae.rda")) sig.diff <- read.csv("result/getMethdiff.hypo.probes.significant.csv") pair <- read.csv("result/getPair.hypo.pairs.significant.csv") head(pair) # significantly hypomethylated probes with putative target genes # Identify enriched motif for significantly hypomethylated probes which # have putative target genes. enriched.motif <- get.enriched.motif( data = mae, probes = pair$Probe, dir.out = "result", label = "hypo", min.incidence = 10, lower.OR = 1.1 ) ## ----eval=TRUE, message=FALSE, warning = FALSE-------------------------------- names(enriched.motif) # enriched motifs head(enriched.motif[names(enriched.motif)[1]]) ## probes in the given set that have the first motif. # get.enriched.motif automatically save output files. # getMotif.hypo.enriched.motifs.rda contains enriched motifs and the probes with the motif. # getMotif.hypo.motif.enrichment.csv contains summary of enriched motifs. dir(path = "result", pattern = "getMotif") # motif enrichment figure will be automatically generated. dir(path = "result", pattern = "motif.enrichment.pdf")