getCellPopMatrix

<code>getCellPopMatrix</code> pulls out the SampleTileMatrix of tiles
 called in one given cell population.

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

getCellPopMatrix function

<dl><dt>SampleTileObj</dt>
<dd>The output from getSampleTileMatrix, a
SummarizedExperiment of pseudobulk intensities across all tiles &amp; cell
types.</dd>
<dt>cellPopulation</dt>
<dd>The cell population you want to pull out.</dd>
<dt>dropSamples</dt>
<dd>Boolean flag to determine whether to drop samples that
were too small for peak calling.</dd>
<dt>NAtoZero</dt>
<dd>Boolean flag to determine whether to replace NAs with zero</dd></dl>

Arguments

getCellPopMatrix — getCellPopMatrix

<dl>

<dt>SampleTileObj</dt>
<dd>The output from getSampleTileMatrix, a
SummarizedExperiment of pseudobulk intensities across all tiles &amp; cell
types.</dd>


<dt>cellPopulation</dt>
<dd>The cell population you want to pull out.</dd>


<dt>dropSamples</dt>
<dd>Boolean flag to determine whether to drop samples that
were too small for peak calling.</dd>


<dt>NAtoZero</dt>
<dd>Boolean flag to determine whether to replace NAs with zero</dd>

</dl>

getCellPopMatrix: `getCellPopMatrix`

Description

Usage

Value

Arguments