## ----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()