deconv.spots

deconv.spots,SpatialDDLS-method

deconv.spots&lt;-

deconv.spots&lt;-,SpatialDDLS-method

Get and set <code>deconv.spots</code> slot in a
<code>SpatialDDLS</code> object

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

deconv.spots function

<dl><dt>object</dt>
<dd><code>SpatialDDLS</code> object.</dd>
<dt>index.st</dt>
<dd>Name or index of predicted cell proportions (same as for the
<code>spatial.experiments</code> slot). If <code>NULL</code> (by default), all
results are returned.</dd>
<dt>value</dt>
<dd>List of predicted cell type proportions for the experiments
stored in the <code>spatial.experiments</code> slot.</dd></dl>

Arguments

Get and set deconv.spots slot in a
SpatialDDLS object — deconv.spots

<dl>

<dt>object</dt>
<dd><code>SpatialDDLS</code> object.</dd>


<dt>index.st</dt>
<dd>Name or index of predicted cell proportions (same as for the
<code>spatial.experiments</code> slot). If <code>NULL</code> (by default), all
results are returned.</dd>


<dt>value</dt>
<dd>List of predicted cell type proportions for the experiments
stored in the <code>spatial.experiments</code> slot.</dd>

</dl>

deconv.spots: Get and set `deconv.spots` slot in a `SpatialDDLS` object

Description

Usage

Arguments