SetWandHfromWHinitials

Use values calculated in the step to determine number of latent factors in the initial
steps for the jrSiCKLSNMF algorithm. If only a subset was calculated, this produces an error.
In this case, please use <code>GenerateWmatricesandHmatrix</code> to generate new
\(\mathbf{W}^v\) matrices and a new \(\mathbf{H}\) matrix.

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

SetWandHfromWHinitials function

<dl><dt>SickleJr</dt>
<dd>An object of class SickleJr</dd>
<dt>d</dt>
<dd>The number of desired latent factors</dd></dl>

Arguments

Set \(\mathbf{W}\) matrices and \(\mathbf{H}\) matrix from pre-calculated values — SetWandHfromWHinitials

<dl>

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


<dt>d</dt>
<dd>The number of desired latent factors</dd>

</dl>

SetWandHfromWHinitials: Set \(\mathbf{W}\) matrices and \(\mathbf{H}\) matrix from pre-calculated values

Description

Usage

Value

Arguments

Examples