## ----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------------------------------------------------------------ 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()