## ----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)) ## ----eval=FALSE, message=FALSE------------------------------------------------ # library(ELMER) # # example input # met <- matrix(rep(0,15),ncol = 5) # colnames(met) <- c( # "Sample1", # "Sample2", # "Sample3", # "Sample4", # "Sample5" # ) # rownames(met) <- c("cg26928153","cg16269199","cg13869341") # # exp <- matrix(rep(0,15),ncol = 5) # colnames(exp) <- c( # "Sample1", # "Sample2", # "Sample3", # "Sample4", # "Sample5" # ) # rownames(exp) <- c("ENSG00000073282","ENSG00000078900","ENSG00000141510") # # # assay <- c( # rep("DNA methylation", ncol(met)), # rep("Gene expression", ncol(exp)) # ) # primary <- c(colnames(met),colnames(exp)) # colname <- c(colnames(met),colnames(exp)) # sampleMap <- data.frame(assay,primary,colname) # # distal.probes <- get.feature.probe( # genome = "hg19", # met.platform = "EPIC" # ) # # colData <- data.frame(sample = colnames(met)) # rownames(colData) <- colnames(met) # # mae <- createMAE( # exp = exp, # met = met, # save = TRUE, # filter.probes = distal.probes, # colData = colData, # sampleMap = sampleMap, # linearize.exp = TRUE, # save.filename = "mae.rda", # met.platform = "EPIC", # genome = "hg19", # TCGA = FALSE # )