SimData

A simulated dataset with $\mathcal{U}(1,1.25)$ multiplicative noise for the
scRNA-seq variability parameter in SPARSim for the simulated scRNA-seq data and
with $\mathcal{N}(-0.25,0.25)$ additive noise to the expression levels of the scATAC-seq data
for data simulated via SimATAC. The simulated matrices are located in SimData$Xmatrices
and the identities for the cell types are contained in SimData$cell_type. This corresponds
to the Xmatrix data found in both
XandLmatrices25/XandindividLKNNLmatrices1Sparsity5.RData and
XandBulkLmatrix25/XandBulkLKNNmatrices1Sparsity5.RData on our Github
<a href="https://github.com/ellisdoro/jrSiCKLSNMF_Simulations">ellisdoro/jrSiCKLSNMF_Simulations</a>

datasets

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

SimData function

A list made up of a two items. The first is list of 2 simulated sparse matrices
and the second is a vector containing cell identities.<dl>
<dt>Xmatrices</dt>
<dd>A list of 2 sparse matrices, each containing a different
simulated omics modality measured on the same set of single cells: the first entry in the list
corresponds to simulated scRNA-seq data and has 1000 genes and 300 cells; the second entry in
the list corresponds to simulated scATAC-seq data and has 5910 peaks and 300
cells.</dd><dt>cell_type</dt>
<dd>A vector containing the cell-type identities of the simulated data</dd></dl>

Format

A simulated dataset with $\mathcal{U}(1,1.25)$ multiplicative noise for the
scRNA-seq variability parameter in SPARSim for the simulated scRNA-seq data and
with $\mathcal{N}(-0.25,0.25)$ additive noise to the expression levels of the scATAC-seq data
for data simulated via SimATAC. The simulated matrices are located in SimData$Xmatrices
and the identities for the cell types are contained in SimData$cell_type. This corresponds
to the Xmatrix data found in both
XandLmatrices25/XandindividLKNNLmatrices1Sparsity5.RData and
XandBulkLmatrix25/XandBulkLKNNmatrices1Sparsity5.RData on our Github
<a href='https://github.com/ellisdoro/jrSiCKLSNMF_Simulations'>ellisdoro/jrSiCKLSNMF_Simulations</a>

A simulated dataset for use with jrSiCKLSNMF — SimData

A list made up of a two items. The first is list of 2 simulated sparse matrices
and the second is a vector containing cell identities.<dl>
<dt>Xmatrices</dt>
<dd>A list of 2 sparse matrices, each containing a different
simulated omics modality measured on the same set of single cells: the first entry in the list
corresponds to simulated scRNA-seq data and has 1000 genes and 300 cells; the second entry in
the list corresponds to simulated scATAC-seq data and has 5910 peaks and 300
cells.</dd>

<dt>cell_type</dt>
<dd>A vector containing the cell-type identities of the simulated data</dd>

</dl>

SimData: A simulated dataset for use with jrSiCKLSNMF

Description

Usage

Arguments

Format