H5matref {BiocSklearn} | R Documentation

## obtain an HDF5 dataset reference suitable for handling as numpy matrix

### Description

obtain an HDF5 dataset reference suitable for handling as numpy matrix

### Usage

    H5matref(filename, dsname = "assay001")

### Arguments

`filename` | a pathname to an HDF5 file
`dsname` | internal name of HDF5 matrix to use, defaults to 'assay001'

### Value

instance of (S3) "h5py._hl.dataset.Dataset"

### Examples

    fn = system.file("ban_6_17/assays.h5", package="BiocSklearn")
    ban = H5matref(fn)
    ban
    np = import("numpy", convert=FALSE) # ensure
    ban$shape
    np$take(ban, 0:3, 0L)
    fullpca = skPCA(ban)
    dim(getTransformed(fullpca))
    ta = np$take
    # project samples
    ta(ban, 0:20, 0L)$shape
    st = skPartialPCA_step(ta(ban, 0:20, 0L))
    st = skPartialPCA_step(ta(ban, 21:40, 0L), obj=st)
    st = skPartialPCA_step(ta(ban, 41:63, 0L), obj=st)
    oo = st$transform(ban)
    dim(oo)
    cor(oo[,1:4], getTransformed(fullpca)[,1:4])

[Package BiocSklearn version 1.2.0 Index]