bulkUMAP

<code>bulkUMAP</code> generates UMAP from pseudobulk LSIObj object, and merges in metadata.

A statistical framework and analysis tool for open chromatin
analysis designed specifically for single cell ATAC-seq (Assay for
Transposase-Accessible Chromatin) data, after cell type/cluster
identification. These novel modules remove unwanted technical variation,
identify open chromatin, robustly models repeated measures in single cell
data, implement advanced statistical frameworks to model zero-inflation for
differential and co-accessibility analyses, and integrate with existing
databases and modules for downstream analyses to reveal biological insights.
MOCHA provides a statistical foundation for complex downstream analysis to
help advance the potential of single cell ATAC-seq for applied studies.
Methods for zero-inflated statistics are as described in:
Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>.
Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated
Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Imran McGrath

MOCHA

Modeling for Single-Cell Open Chromatin Analysis

Samir Rachid Zaim

Mark-Phillip Pebworth

Lauren Okada

Xiaojun Li

bulkUMAP function

<dl><dt>SEObj</dt>
<dd>The SummarizedExperiment object output from bulkDimReduction, or an STM, subsetted down to just one cell type.</dd>
<dt>assay</dt>
<dd>A string, describing the name of the assay within SEObj to run UMAP ('PCA', 'LSI', or 'counts').</dd>
<dt>components</dt>
<dd>A vector of integers. Number of components to include in LSI (1:30 typically).</dd>
<dt>nNeighbors</dt>
<dd>See umap. The size of local neighborhood (in terms of number of
neighboring sample points) used for manifold approximation. Default is 15.</dd>
<dt>returnModel</dt>
<dd>A boolean. Default is FALSE. If set to true, it will return a list, where the first is the UMAP coordinates with metadata for plotting, and the second is the full UMAP model so further projection can occur.</dd>
<dt>seed</dt>
<dd>an integer. Represents the random seed to pass to the UMAP. Default seed is 1.</dd>
<dt>...</dt>
<dd>Additional arguments to be passed to umap.</dd></dl>

Arguments

bulkUMAP — bulkUMAP

<dl>

<dt>SEObj</dt>
<dd>The SummarizedExperiment object output from bulkDimReduction, or an STM, subsetted down to just one cell type.</dd>


<dt>assay</dt>
<dd>A string, describing the name of the assay within SEObj to run UMAP ('PCA', 'LSI', or 'counts').</dd>


<dt>components</dt>
<dd>A vector of integers. Number of components to include in LSI (1:30 typically).</dd>


<dt>nNeighbors</dt>
<dd>See umap. The size of local neighborhood (in terms of number of
neighboring sample points) used for manifold approximation. Default is 15.</dd>


<dt>returnModel</dt>
<dd>A boolean. Default is FALSE. If set to true, it will return a list, where the first is the UMAP coordinates with metadata for plotting, and the second is the full UMAP model so further projection can occur.</dd>


<dt>seed</dt>
<dd>an integer. Represents the random seed to pass to the UMAP. Default seed is 1.</dd>


<dt>...</dt>
<dd>Additional arguments to be passed to umap.</dd>

</dl>

bulkUMAP: `bulkUMAP`

Description

Usage

Value

Arguments

Examples