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

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

## ---- 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)

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/screenshot_qc.png")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/screenshot_design.png")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/screenshot_sexprediction.png")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/screenshot_pca.png")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/screenshot_designbias.png")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/All.png")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/BothPlate.jpg")

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("figures/BothStatus.jpg")

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