## ---- echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE-------------------- library(ELMER) library(DT) library(dplyr) library(BiocStyle) ## ----eval=TRUE, message=FALSE, warning = FALSE, results = "hide"-------------- mae <- get(load("mae.rda")) sig.diff <- get.diff.meth(data = mae, group.col = "definition", group1 = "Primary solid Tumor", group2 = "Solid Tissue Normal", minSubgroupFrac = 0.2, # if supervised mode set to 1 sig.dif = 0.3, diff.dir = "hypo", # Search for hypomethylated probes in group 1 cores = 1, dir.out ="result", pvalue = 0.01) ## ----eval=TRUE, message=FALSE, warning = FALSE-------------------------------- head(sig.diff) %>% datatable(options = list(scrollX = TRUE)) # get.diff.meth automatically save output files. # - getMethdiff.hypo.probes.csv contains statistics for all the probes. # - getMethdiff.hypo.probes.significant.csv contains only the significant probes which # is the same with sig.diff # - a volcano plot with the diff mean and significance levels dir(path = "result", pattern = "getMethdiff") ## ----eval=TRUE, message=FALSE, warning = FALSE,echo=FALSE--------------------- group1 <- "Primary solid Tumor" group2 <- "Solid Tissue Normal" out <- readr::read_csv(dir(path = "result", pattern = "getMethdiff.hypo.probes.csv",full.names = TRUE)) TCGAbiolinks:::TCGAVisualize_volcano(x = as.data.frame(out)[,grep("Minus",colnames(out),value = T)], y = out$adjust.p, title = paste0("Volcano plot - Probes ", "hypomethylated in ", group1, " vs ", group2,"\n"), filename = NULL, label = c("Not Significant", paste0("Hypermethylated in ",group1), paste0("Hypomethylated in ",group1)), ylab = expression(paste(-Log[10], " (FDR corrected P-values) [one tailed test]")), xlab = expression(paste( "DNA Methylation difference (",beta,"-values)") ), x.cut = 0.3, y.cut = 0.01)