Nothing
## ---- 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()
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