saveTrainedModelAsH5

Save a trained <code>SpatialDDLS</code> deep neural network model to
disk as an HDF5 file. Note that this function does not save the
<code>DeconvDLModel</code> object, only the trained keras
model. This is the alternative to the <code><a href="/link/saveRDS?package=SpatialDDLS&version=1.0.1" data-mini-rdoc="SpatialDDLS::saveRDS">saveRDS</a></code> and
<code>preparingToSave</code> functions if you want to keep the state of the
optimizer.

Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.

Diego Ma<c3><b1>anes

SpatialDDLS

Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks

Diego Mañanes

Carlos Torroja

Fatima Sanchez-Cabo

saveTrainedModelAsH5 function

<dl><dt>object</dt>
<dd><code>SpatialDDLS</code> object with
<code>trained.model</code> slot.</dd>
<dt>file.path</dt>
<dd>Valid file path where to save the model to.</dd>
<dt>overwrite</dt>
<dd>Overwrite file if it already exists.</dd></dl>

Arguments

Save a trained <code>SpatialDDLS</code> deep neural network model to
disk as an HDF5 file. Note that this function does not save the
<code>DeconvDLModel</code> object, only the trained keras
model. This is the alternative to the <code><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></code> and
<code>preparingToSave</code> functions if you want to keep the state of the
optimizer.

Save a trained SpatialDDLS deep neural network model to
disk as an HDF5 file — saveTrainedModelAsH5

<dl>

<dt>object</dt>
<dd><code>SpatialDDLS</code> object with
<code>trained.model</code> slot.</dd>


<dt>file.path</dt>
<dd>Valid file path where to save the model to.</dd>


<dt>overwrite</dt>
<dd>Overwrite file if it already exists.</dd>

</dl>

saveTrainedModelAsH5: Save a trained `SpatialDDLS` deep neural network model to disk as an HDF5 file

Description

Usage

Value

Arguments

See Also