scINSIGHT-class

scINSIGHT

The scINSIGHT object is created from two or more single cell datasets. To construct a
scINSIGHT object, the user needs to provide at least two normalized expression (or another
single-cell modality) matrices and the condition vector.

We develop a novel matrix factorization tool named 'scINSIGHT' to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. Given multiple gene expression samples from different biological conditions, 'scINSIGHT' simultaneously identifies common and condition-specific gene modules and quantify their expression levels in each sample in a lower-dimensional space. With the factorized results, the inferred expression levels and memberships of common gene modules can be used to cluster cells and detect cell identities, and the condition-specific gene modules can help compare functional differences in transcriptomes from distinct conditions. Please also see Qian K, Fu SW, Li HW, Li WV (2022) <doi:10.1186/s13059-022-02649-3>.

Kun Qian

Interpretation of Heterogeneous Single-Cell Gene Expression Data

Wei Vivian Li

scINSIGHT-class function

<dl>
<dt><code>norm.data</code></dt>
<dd>List of normalized expression matrices (genes by cells). Each matrix should have the same number and name of genes.</dd></dl>
<dt><code>condition</code></dt>
<dd>Vector specifying each sample's condition name.</dd>
<dt><code>W_1</code></dt>
<dd>List of \(W_{\ell1}\) estimated by scINSIGHT, names correspond to sample names.</dd>
<dt><code>W_2</code></dt>
<dd>List of \(W_{\ell2}\) estimated by scINSIGHT, names correspond to sample names.</dd>
<dt><code>H</code></dt>
<dd>List of \(H\) estimated by scINSIGHT, names correspond to condition names.</dd>
<dt><code>V</code></dt>
<dd>Matrix \(V\) estimated by scINSIGHT.</dd>
<dt><code>norm.W_2</code></dt>
<dd>List of \(W_{\ell2}\) after normalization. Recommended for downstream analysis.</dd>
<dt><code>clusters</code></dt>
<dd>List of cluster results.</dd>
<dt><code>parameters</code></dt>
<dd>List of selected parameters, including \(K\) and \(\lambda\).</dd>

Slots

The scINSIGHT Class — scINSIGHT-class

<dl>
<dt><code>norm.data</code></dt>
<dd>List of normalized expression matrices (genes by cells). Each matrix should have the same number and name of genes.</dd>


<dt><code>condition</code></dt>
<dd>Vector specifying each sample's condition name.</dd>


<dt><code>W_1</code></dt>
<dd>List of \(W_{\ell1}\) estimated by scINSIGHT, names correspond to sample names.</dd>


<dt><code>W_2</code></dt>
<dd>List of \(W_{\ell2}\) estimated by scINSIGHT, names correspond to sample names.</dd>


<dt><code>H</code></dt>
<dd>List of \(H\) estimated by scINSIGHT, names correspond to condition names.</dd>


<dt><code>V</code></dt>
<dd>Matrix \(V\) estimated by scINSIGHT.</dd>


<dt><code>norm.W_2</code></dt>
<dd>List of \(W_{\ell2}\) after normalization. Recommended for downstream analysis.</dd>


<dt><code>clusters</code></dt>
<dd>List of cluster results.</dd>


<dt><code>parameters</code></dt>
<dd>List of selected parameters, including \(K\) and \(\lambda\).</dd>


</dl>

scINSIGHT-class: The scINSIGHT Class

Description

Arguments

Slots

Details