h5mat {BiocSklearn} | R Documentation

## 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)
    }

[Package BiocSklearn version 1.10.3 Index]