DNAmetNorm.R

deps <- c("shiny","shinyFiles","methylumi")
for(pkg in deps)  if (!pkg %in% installed.packages()) biocLite(pkg, dependencies = TRUE)
library(shiny)
library(shinyFiles)
library(methylumi)

ui <- pageWithSidebar(
  headerPanel(
    'DNA methylation idat normalization with methylumi',
    'methylumi normalization'
  ),
  sidebarPanel(
    shinyFilesButton('file', 'Select idat files', 'Please select a file', TRUE),
    actionButton("normalize",
                 "Normalize",
                 style = "background-color: #000080;
                                        color: #FFFFFF;
                                        margin-left: auto;
                                        margin-right: auto;
                                        width: auto",
                 icon = icon("flask"))
  ),
  mainPanel(
    tags$h4('The output of a file selection'),
    tags$p(HTML('Files selected:')),
    verbatimTextOutput('filepaths')
  )
)


server <- function(input, output, session) {
  volumes <- c(wd="./",home=Sys.getenv("HOME"), getVolumes()(), temp=tempdir())
  # A notification ID
  shinyFileChoose(input, 'file', roots=volumes, session=session, restrictions=system.file(package='base'),filetypes=c('', 'idat'))
  output$filepaths <- renderPrint({parseFilePaths(volumes, input$file)})
  
  observeEvent(input$normalize, {
    files <- as.character(parseFilePaths(volumes, isolate({input$file}))$datapath)
    withProgress(message = 'Calculation in progress',
                 detail = 'This may take a while...', value = 0, {
                   incProgress(1/4,message = "Reading data")
                   idat <- methylumIDAT(unique(gsub("_Red.idat|_Grn.idat","",basename(files))),idatPath = unique(dirname(files)))
                   incProgress(1/4,message = "Normalizing data")
                   proc <- stripOOB(normalizeMethyLumiSet(methylumi.bgcorr(idat)))
                   betaValue <- betas(proc)
                   incProgress(1/4,message = "Saving results")
                   save(betaValue, file="betaValues.Rda")
                 })
    showNotification("File saved as: betaValues.Rda", duration = NULL)
  })
  
}
shinyApp(ui = ui, server = server)