## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------
BiocStyle::latex()

## ----shinyMethylData, eval=FALSE-----------------------------------------
## library(shinyMethyl)
## library(shinyMethylData)
## runShinyMethyl(summary.tcga.raw, summary.tcga.norm)

## ----minfidata,eval=TRUE,warning=FALSE,message=FALSE---------------------
library(minfiData)

## ----2stepapproach,eval=TRUE,message=FALSE,warning=FALSE-----------------
library(shinyMethyl)
summary <- shinySummarize(RGsetEx) 

## ----launching,eval=FALSE------------------------------------------------
## runShinyMethyl(summary)

## ----loadlibraries, eval=TRUE, results="hide",warning=FALSE,message=FALSE----
library(minfiData)
library(minfi)

## ----basedir,eval=FALSE--------------------------------------------------
## baseDir <- system.file("extdata", package = "minfiData")
## # baseDir <- "/home/yourDirectoryPath"

## ----experimentsheet,eval=FALSE------------------------------------------
## targets <- read.450k.sheet(baseDir)
## head(targets)

## ----rgsetconstruction,eval=FALSE----------------------------------------
## RGSet <- read.450k.exp(base = baseDir, targets = targets)

## ----phenotype, eval=FALSE-----------------------------------------------
## pd <- pData(RGSet)
## head(pd)

## ----summarize, eval=FALSE-----------------------------------------------
## myShinyMethylSet <- shinySummarize(RGSet)

## ----sessionLaunching, eval=FALSE----------------------------------------
## runShinyMethyl(myShinyMethylSet)

## ----normalize, eval=FALSE-----------------------------------------------
## GRSet.norm <- preprocessQuantile(RGSet)

## ----summarizeNorm,eval=FALSE--------------------------------------------
## summary   <- shinySummarize(RGSset)
## summary.norm <- shinySummarize(GRSet.norm)

## ----runshiny,eval=FALSE-------------------------------------------------
## runShinyMethyl(summary, summary.norm)

## ----eval=TRUE,warning=FALSE,message=FALSE-------------------------------
library(shinyMethyl)
library(shinyMethylData)
slotNames(summary.tcga.raw)

## ----pheno,eval=TRUE-----------------------------------------------------
head(summary.tcga.raw@phenotype)

## ----sessionInfo, results="asis", echo=FALSE, eval=TRUE------------------
toLatex(sessionInfo())