inst/doc/analysis_data_input.R

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

## ---- 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)