## ---- 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()