## ----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")) ## ----results='hide', echo=TRUE, message=FALSE, warning=FALSE, fig.height=5, fig.cap="Each scatter plot shows the methylation level of an example probe cg19403323 in all LUSC samples plotted against the expression of one of 20 adjacent genes."---- scatter.plot(data = mae, byProbe = list(probe = c("cg19403323"), numFlankingGenes = 20), category = "definition", lm = TRUE, # Draw linear regression curve save = FALSE) ## ----results='hide',eval=TRUE, fig.cap="Scatter plot shows the methylation level of an example probe cg19403323 in all LUSC samples plotted against the expression of the putative target gene SYT14."---- scatter.plot(data = mae, byPair = list(probe = c("cg19403323"), gene = c("ENSG00000143469")), category = "definition", save = TRUE, lm_line = TRUE) ## ----eval=TRUE, warning=FALSE, fig.cap="Each scatter plot shows the average methylation level of sites with the first enriched motif in all LUSC samples plotted against the expression of the transcription factor TP53, SOX2 respectively."---- load("result/getMotif.hypo.enriched.motifs.rda") names(enriched.motif)[1] scatter.plot(data = mae, byTF = list(TF = c("TP53","SOX2"), probe = enriched.motif[[names(enriched.motif)[1]]]), category = "definition", save = TRUE, lm_line = TRUE)