BuildSNNGraphLaplacians

Generate graph Laplacians for graph regularization of
jrSiCKLSNMF from the list of raw count matrices using an SNN graph. SNN is more robust to
situations where the number of cells outnumbers the number of features. Uses
the <code>scran</code> package's <code>BuildSNNGraph</code> function Lun2016jrSiCKLSNMF

Methods to perform Joint graph Regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization ('jrSiCKLSNMF', pronounced "junior sickles NMF") on quality controlled single-cell multimodal omics count data. 'jrSiCKLSNMF' specifically deals with dual-assay scRNA-seq and scATAC-seq data. This package contains functions to extract meaningful latent factors that are shared across omics modalities. These factors enable accurate cell-type clustering and facilitate visualizations. Methods for pre-processing, clustering, and mini-batch updates and other adaptations for larger datasets are also included. For further details on the methods used in this package please see Ellis, Roy, and Datta (2023) <doi:10.3389/fgene.2023.1179439>.

Dorothy Ellis

jrSiCKLSNMF

Multimodal Single-Cell Omics Dimensionality Reduction

Susmita Datta

Kenneth Perkins

Renaud Gaujoux

BuildSNNGraphLaplacians function

<dl><dt>SickleJr</dt>
<dd>An object of class SickleJr</dd>
<dt>k</dt>
<dd>Number of KNN neighbors to calculate SNN graph; defaults to 20</dd></dl>

Arguments

Build SNN graphs and generate their graph Laplacians — BuildSNNGraphLaplacians

<dl>

<dt>SickleJr</dt>
<dd>An object of class SickleJr</dd>


<dt>k</dt>
<dd>Number of KNN neighbors to calculate SNN graph; defaults to 20</dd>

</dl>

BuildSNNGraphLaplacians: Build SNN graphs and generate their graph Laplacians

Description

Usage

Value

Arguments

References

Examples