h5mat: create a file connection to HDF5 matrix

In vjcitn/BiocSklearn: interface to python sklearn via Rstudio reticulate

create a file connection to HDF5 matrix

Description

create a file connection to HDF5 matrix

Usage

h5mat(infile, mode = "r", ...)

Arguments

infile	a pathname to an HDF5 file
mode	character(1) defaults to "r", see py_help for h5py.File
...	unused

Value

instance of (S3) h5py._hl.files.File

Note

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.

Examples

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)
}

vjcitn/BiocSklearn documentation built on Feb. 4, 2024, 5:12 a.m.