## ----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())