## ---- message = FALSE------------------------------------------------------ library(minfi) minfiDataDir <- system.file("extdata", package = "minfiData") targets <- read.metharray.sheet(minfiDataDir, verbose = FALSE) RGset <- read.metharray.exp(targets = targets) ## ---- message=FALSE-------------------------------------------------------- library(FlowSorted.Blood.450k) library(mCSEA) data(mcseadata) cellCounts = estimateCellCounts(RGset) print(cellCounts) ## ---- message = FALSE, results='hide'-------------------------------------- library(mCSEA) data(mcseadata) ## -------------------------------------------------------------------------- head(betaTest, 3) print(phenoTest) ## -------------------------------------------------------------------------- myRank <- rankProbes(betaTest, phenoTest, refGroup = "Control") ## -------------------------------------------------------------------------- head(myRank) ## ---- warning=FALSE-------------------------------------------------------- set.seed(123) myResults <- mCSEATest(myRank, betaTest, phenoTest, regionsTypes = "promoters", platform = "EPIC") ## -------------------------------------------------------------------------- ls(myResults) ## -------------------------------------------------------------------------- head(myResults[["promoters"]][,-7]) ## -------------------------------------------------------------------------- head(myResults[["promoters_association"]], 3) ## -------------------------------------------------------------------------- head(assocGenes450k, 3) ## ---- message = FALSE, results='hide'-------------------------------------- mCSEAPlot(myResults, regionType = "promoters", dmrName = "CLIC6", transcriptAnnotation = "symbol", makePDF = FALSE) ## -------------------------------------------------------------------------- mCSEAPlotGSEA(myRank, myResults, regionType = "promoters", dmrName = "CLIC6") ## -------------------------------------------------------------------------- # Explore expression data head(exprTest, 3) # Run mCSEAIntegrate function resultsInt <- mCSEAIntegrate(myResults, exprTest, "promoters", "ENSEMBL") resultsInt ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()