## ---- echo = false，hide = tri（dplyr）dir.create（“结果”，showwarnings = false）库（biocStyle）## ----消息= false ---------------------------------------------------------------------------------------------------------------------------＃获取远距离探针，远离TSS的远端探针1distal.probes <-get.feature.probe（genome =“ hg19”，met.platform =“ 450k”，rm.chr = paste0（“ chr”，c（2:22，“ x”，“ y”）））## ---------- true，messages = false --------------------------------------------------------------------------------------------------------------------------------------库（MultiasSayExperiment）库（elmer.data）data（lusc_rna_refined，package =“ elmer.data”）data（lusc_meth_refined，package =“ elmer.data”）geneexp [1 geneexp [1：5,1：5] meth [1：5,1：5] mae < - createmae（exp = geneexp，met = meth = meth = meth，save = true，linearize.exp = true，save.filename =“ mae.rda”，filter.probes =远端。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（选项）= list（scrollx = true））as.data.frame（assay（getmet（mae）[1：5,1：5]）））％>％datatable（options = list = list（scrollx = true））## ------------eval = false，消息= false -----------------------------------------------------------------------------------------------------------------------------------------------------------------------＃library（Elmer）＃＃示例输入＃MET <-Matrix（Rep（0,15），NCOL = 5）＃ColNames（MET）<-C（＃“ Sample1”，＃“ sample2”，＃“ sample3”，＃“ sample4”，＃“ sample5”＃）＃rownames（met）< - c（“ CG26928153”，“ CG16269199”，“ CG13869341”）），ncol = 5）＃colnames（exp）<-c（＃“ sample1”，＃“ sample2”，＃“ sample3”，＃“ sample4”，＃“ sample5”＃）＃rownames（exp）<-c（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 # )