plotConsensus

<code>plotConsensus</code> Extracts the peak reproducibility and generates a
					heuristic plots that can be used to determine the reproducibility threshold
					used within getSampleTileMatrix.

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

plotConsensus function

<dl><dt>tileObject</dt>
<dd>A MultiAssayExperiment object from callOpenTiles,</dd>
<dt>cellPopulations</dt>
<dd>the cell populations you want to visualize.</dd>
<dt>groupColumn</dt>
<dd>Optional parameter, same as in getSampleTileMatrix, which defines whether you
want to plot reproducibility within each</dd>
<dt>returnPlotList</dt>
<dd>Instead of one plot with all celltypes/conditions, it returns a list of plots for each cell types</dd>
<dt>returnDFs</dt>
<dd>Instead of a plot, returns a data.frame of the reproducibility across samples.
If set to false, then it plots the data.frame instead of returning it.</dd>
<dt>numCores</dt>
<dd>Number of cores to multithread over.</dd></dl>

Arguments

plotConsensus — plotConsensus

<dl>

<dt>tileObject</dt>
<dd>A MultiAssayExperiment object from callOpenTiles,</dd>


<dt>cellPopulations</dt>
<dd>the cell populations you want to visualize.</dd>


<dt>groupColumn</dt>
<dd>Optional parameter, same as in getSampleTileMatrix, which defines whether you
want to plot reproducibility within each</dd>


<dt>returnPlotList</dt>
<dd>Instead of one plot with all celltypes/conditions, it returns a list of plots for each cell types</dd>


<dt>returnDFs</dt>
<dd>Instead of a plot, returns a data.frame of the reproducibility across samples.
If set to false, then it plots the data.frame instead of returning it.</dd>


<dt>numCores</dt>
<dd>Number of cores to multithread over.</dd>

</dl>

plotConsensus: `plotConsensus`

Description

Usage

Value

Arguments