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'

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 1.0.2 Index]