combineSampleTileMatrix

<code>combineSampleTileMatrix</code> combines all celltypes in a
 SampleTileMatrix object into a SummarizedExperiment with one single matrix
 across all cell types and samples,

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

combineSampleTileMatrix function

<dl><dt>SampleTileObj</dt>
<dd>The SummarizedExperiment object output from
getSampleTileMatrix containing your sample-tile matrices</dd>
<dt>NAtoZero</dt>
<dd>Set NA values in the sample-tile matrix to zero</dd>
<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd></dl>

Arguments

combineSampleTileMatrix — combineSampleTileMatrix

<dl>

<dt>SampleTileObj</dt>
<dd>The SummarizedExperiment object output from
getSampleTileMatrix containing your sample-tile matrices</dd>


<dt>NAtoZero</dt>
<dd>Set NA values in the sample-tile matrix to zero</dd>


<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd>

</dl>

combineSampleTileMatrix: `combineSampleTileMatrix`

Description

Usage

Value

Arguments