colMins

colMins.HDF5Matrix

rowMins

rowMins.HDF5Matrix

Block-wise computation of column and row minimums.

A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, and QR decomposition) written in C++ and R, along with building
blocks from which higher-level multivariate methods such as canonical
correlation analysis can be constructed. These building blocks are designed
not only for direct use, but also as foundational components for developing
new statistical methods that must operate on datasets too large to fit in
memory. The package supports data provided either as 'HDF5' files or
standard R objects, and is intended for high-dimensional applications such
as 'omics' and precision-medicine research.

Dolors Pelegri-Siso

BigDataStatMeth

Scalable Statistical Computing with HDF5-Backed Matrices

Juan R. Gonzalez

colMins function

<dl><dt>x</dt>
<dd>An <code>HDF5Matrix</code> object.</dd>
<dt>...</dt>
<dd>Ignored.</dd>
<dt>paral</dt>
<dd>Logical or NULL. Enable OpenMP parallelisation.</dd>
<dt>wsize</dt>
<dd>Integer or NULL. Block size for HDF5 reads (NULL = auto).</dd>
<dt>threads</dt>
<dd>Integer or NULL. Number of OpenMP threads (NULL = auto).</dd>
<dt>save_to</dt>
<dd>Where to save the result (see Details). NULL returns a
plain R vector; a character string <code>"group/dataset"</code>
saves in the same file as <code>x</code>; a named list
<code>list(file = "f.h5", path = "group/dataset")</code> saves in
a different file. In both non-NULL cases an
<code>HDF5Matrix</code> handle is returned.</dd>
<dt>overwrite</dt>
<dd>Logical. Overwrite an existing dataset at <code>save_to</code>?
(Currently always TRUE when <code>save_to</code> is not NULL.)</dd></dl>

Arguments

Column and row minimums for HDF5Matrix — colMins

<dl>

<dt>x</dt>
<dd>An <code>HDF5Matrix</code> object.</dd>


<dt>...</dt>
<dd>Ignored.</dd>


<dt>paral</dt>
<dd>Logical or NULL. Enable OpenMP parallelisation.</dd>


<dt>wsize</dt>
<dd>Integer or NULL. Block size for HDF5 reads (NULL = auto).</dd>


<dt>threads</dt>
<dd>Integer or NULL. Number of OpenMP threads (NULL = auto).</dd>


<dt>save_to</dt>
<dd>Where to save the result (see Details). NULL returns a
plain R vector; a character string <code>"group/dataset"</code>
saves in the same file as <code>x</code>; a named list
<code>list(file = "f.h5", path = "group/dataset")</code> saves in
a different file. In both non-NULL cases an
<code>HDF5Matrix</code> handle is returned.</dd>


<dt>overwrite</dt>
<dd>Logical. Overwrite an existing dataset at <code>save_to</code>?
(Currently always TRUE when <code>save_to</code> is not NULL.)</dd>

</dl>

colMins: Column and row minimums for HDF5Matrix

Description

Usage

Value

Arguments