read.methdf5: process an IDATs directly into an RGChannelSet backed by HDF5

In trichelab/h5testR: Tests for HDF5-backed DNAme, RNAseq, and MultiAssayExperiment objects

Description

For processing entire sample sheets, see read.methdf5.sheet

Usage

read.methdf5(basenames, filepath = "my_h5_se", ...)

Arguments

basenames	basename(s) (i.e., path(s) to pair(s) of IDAT files)
filepath	a directory in which to put the HDF5 data ("my_h5_se")
...	other arguments, passed to minfi:::read.metharray2

Value

an HDF5-backed RGChannelSet

See Also

read.methdf5.sheet

Examples

# cheezy 450k example
if (require("minfiData")) {
  baseDir <- system.file("extdata", package = "minfiData")
  sheet <- read.metharray.sheet(baseDir)
  inCore <- read.metharray(basenames=sheet[1, "Basename", drop=FALSE])
  outOfCore <- read.methdf5(basenames=sheet[1, "Basename", drop=FALSE])
  stopifnot(identical(dim(inCore), dim(outOfCore)))
  verifyRGsets(ram=inCore, hdf5=outOfCore)
}

# set TRUE for real test
RUN_TARGET_EPIC <- FALSE

# the real thing, with TARGET AML data
# yes all 500 will run on your laptop.
# no it will not be particularly fast.
# be certain that you have disk space!
if (RUN_TARGET_EPIC) {

  if (!file.exists("GSE124413/GSE124413_RAW.tar")) {
    message("Warning: you are about to download 7GB of compressed IDATs.") 
    message("Exit *NOW* if you do not have the space or desire to do so.")
    GEOquery::getGEOSuppFiles("GSE124413") 
  } 

  # ...time passes...
  if (length(list.files(patt="GSM3532678_200989060236_R08C01_")) < 2) {
    utils::untar("GSE124413/GSE124413_RAW.tar")
  }

}

# how many arrays to test on? 10? 50? All 500? 
RUN_TARGET_HOWMANY <- 10 

if (RUN_TARGET_EPIC) { 

  set.seed(123) 
  files <- list.files(patt="idat.gz")))
  stubs <- unique(gsub("_(Grn|Red).idat.gz", "", files))
  basenames <- sample(stubs, RUN_TARGET_HOWMANY)

  outOfCore <- read.methdf5(basenames=stubs[indices])
  saveHDF5SummarizedExperiment(outOfCore, dir="TARGET_RGset", replace=TRUE)
  outOfCore <- loadHDF5SummarizedExperiment(dir="TARGET_RGset")
  inCore <- read.metharray(basenames=stubs[indices])

  stopifnot(identical(dim(inCore), dim(outOfCore)))
  verifyRGsets(ram=inCore, hdf5=outOfCore)

} 

trichelab/h5testR documentation built on July 12, 2020, 5:18 p.m.