## ---- echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE--------------- library(ELMER) library(DT) library(dplyr) dir.create("result",showWarnings = FALSE) library(BiocStyle) ## ---- message=FALSE------------------------------------------------------ # get distal probes that are 2kb away from TSS on chromosome 1 distal.probes <- get.feature.probe(genome = "hg19", met.platform = "450K", rm.chr = paste0("chr",c(2:22,"X","Y"))) ## ----eval=TRUE, message=FALSE-------------------------------------------- library(MultiAssayExperiment) library(ELMER.data) data(LUSC_RNA_refined,package = "ELMER.data") data(LUSC_meth_refined,package = "ELMER.data") GeneExp[1:5,1:5] Meth[1:5,1:5] mae <- createMAE(exp = GeneExp, met = Meth, save = TRUE, linearize.exp = TRUE, save.filename = "mae.rda", filter.probes = distal.probes, met.platform = "450K", genome = "hg19", TCGA = TRUE) as.data.frame(colData(mae)[1:5,]) %>% datatable(options = list(scrollX = TRUE)) as.data.frame(sampleMap(mae)[1:5,]) %>% datatable(options = list(scrollX = TRUE)) as.data.frame(assay(getMet(mae)[1:5,1:5])) %>% datatable(options = list(scrollX = TRUE)) as.data.frame(assay(getMet(mae)[1:5,1:5])) %>% datatable(options = list(scrollX = TRUE))