getSequencingBias

<code>getSequencingBias</code> takes the output of peak calling with
 callOpenTiles and creates sample-tile matrices containing the signal
 intensity at each tile.

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

getSequencingBias function

<dl><dt>SampleTileObj</dt>
<dd>a SummarizedExperiment object generated by MOCHA</dd>
<dt>cellPopulations</dt>
<dd>vector of strings. Cell subsets found in the TSAM, or the word 'All' if all should be used.</dd>
<dt>cellPopulation</dt>
<dd>A string denoting the cell population of interest</dd>
<dt>groupColumn</dt>
<dd>The column containing sample group labels</dd>
<dt>foreground</dt>
<dd>The foreground group of samples for differential comparison</dd>
<dt>background</dt>
<dd>The background group of samples for differential comparison</dd>
<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd></dl>

Arguments

getSequencingBias — getSequencingBias

<dl>

<dt>SampleTileObj</dt>
<dd>a SummarizedExperiment object generated by MOCHA</dd>


<dt>cellPopulations</dt>
<dd>vector of strings. Cell subsets found in the TSAM, or the word 'All' if all should be used.</dd>


<dt>cellPopulation</dt>
<dd>A string denoting the cell population of interest</dd>


<dt>groupColumn</dt>
<dd>The column containing sample group labels</dd>


<dt>foreground</dt>
<dd>The foreground group of samples for differential comparison</dd>


<dt>background</dt>
<dd>The background group of samples for differential comparison</dd>


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

</dl>

getSequencingBias: `getSequencingBias`

Description

Usage

Value

Arguments