h5mat {BiocSklearn} | R Documentation |
create a file connection to HDF5 matrix
h5mat(infile, mode = "r", ...)
infile |
a pathname to an HDF5 file |
mode |
character(1) defaults to "r", see py_help for h5py.File |
... |
unused |
instance of (S3) h5py._hl.files.File
The result of this function must be used with basiliskRun with the env argument set to bsklenv, or there is a risk of inconsistent python modules being invoked. This should only be used with the persistent environment discipline of basilisk.
if (interactive()) { # not clear why fn = system.file("ban_6_17/assays.h5", package="BiocSklearn") proc = basilisk::basiliskStart(BiocSklearn:::bsklenv) basilisk::basiliskRun(proc, function(infile, mode="r") { h5py = reticulate::import("h5py") hh = h5py$File( infile, mode=mode ) cat("File reference:\n ") print(hh) cat("File attributes in python:\n ") print(head(names(hh))) cat("File keys in python:\n ") print(hh$keys()) cat("HDF5 dataset in python:\n ") print(hh['assay001']) }, infile=fn, mode="r") basilisk::basiliskStop(proc) }