## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, eval = FALSE)
libv <- c("minfiData", "HDF5Array", "minfi")
sapply(libv, library, character.only = TRUE)

## -----------------------------------------------------------------------------
#  rg.hm450k <- get(data("RGsetEx"))

## -----------------------------------------------------------------------------
#  rg.epic <- convertArray(rg.hm450k, "IlluminaHumanMethylationEPIC")

## -----------------------------------------------------------------------------
#  ms.hm450k <- preprocessRaw(rg) # make MethylSet
#  ms.hm450k <- mapToGenome(ms.hm450k) # make GenomicMethylSet

## -----------------------------------------------------------------------------
#  gr.hm450k <- GenomicMethylSet(gr = granges(ms.hm450k),
#                                Meth = getMeth(ms.hm450k),
#                                Unmeth = getUnmeth(ms.hm450k),
#                                annotation = annotation(ms.hm450k))

## -----------------------------------------------------------------------------
#  saveHDF5SummarizedExperiment(gr.hm450k, dir = "gr_h5se_new")

## -----------------------------------------------------------------------------
#  gr.h5se <- loadHDF5SummarizedExperiment(dir = "gr_h5se_new")

## ----eval = FALSE-------------------------------------------------------------
#  # get flat files
#  m.beta <- getBeta(gr.h5se)
#  anno <- as.data.frame(getAnnotation(gr.h5se))
#  coldata <- as.data.frame(colData(gr.h5se))
#  # save flat files
#  save(m.beta, file = "mbeta_new.rda")
#  save(anno, file = "anno_new.rda")
#  save(coldata, file = "coldata_new.rda")

## ----eval = FALSE-------------------------------------------------------------
#  write.table(m.beta, file = "mbeta_new.txt")
#  write.csv(m.beta, file = "mbeta_new.csv")
#  data.table::fwrite(m.beta, file = "mbeta_new.txt")

## ----eval = FALSE-------------------------------------------------------------
#  save(rg, file = "rg_new.rda")
#  save(gm, file = "gm_new.rda")
#  save(gr, file = "gr_new.rda")

## -----------------------------------------------------------------------------
#  rg.h5se <- rg.h5se[seq(1000),] # subset the h5se object
#  quickResaveHDF5SummarizedExperiment(rg.h5se) # rapidly update stored file