Description Usage Arguments Value See Also Examples
For processing entire sample sheets, see read.methdf5.sheet
1 | read.methdf5(basenames, filepath = "my_h5_se", ...)
|
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 |
an HDF5-backed RGChannelSet
read.methdf5.sheet
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | # 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)
}
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