getPopFrags

<code>getPopFrags</code> returns a list of sample-specific fragments per cell population as a GRangesList.

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

getPopFrags function

<dl><dt>ArchRProj</dt>
<dd>The ArchR Project.</dd>
<dt>cellPopLabel</dt>
<dd>The name of the metadata column of the ArchR Project that contains the populations
of cells you want to extract fragments from.</dd>
<dt>cellSubsets</dt>
<dd>Default is 'ALL'. If you want to export only some populations,
then give it a list of group names. This needs to be unique - no duplicated
names. This list of group names must be identical to names that appear in
the given cellPopLabel metadata column of the ArchR Project.</dd>
<dt>poolSamples</dt>
<dd>Set TRUE to pool sample-specific fragments by cell population. By default this is FALSE and sample-specific fragments are returned.</dd>
<dt>numCores</dt>
<dd>Number of cores to use.</dd>
<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd></dl>

Arguments

Extract fragments by populations from an ArchR Project — getPopFrags

<dl>

<dt>ArchRProj</dt>
<dd>The ArchR Project.</dd>


<dt>cellPopLabel</dt>
<dd>The name of the metadata column of the ArchR Project that contains the populations
of cells you want to extract fragments from.</dd>


<dt>cellSubsets</dt>
<dd>Default is 'ALL'. If you want to export only some populations,
then give it a list of group names. This needs to be unique - no duplicated
names. This list of group names must be identical to names that appear in
the given cellPopLabel metadata column of the ArchR Project.</dd>


<dt>poolSamples</dt>
<dd>Set TRUE to pool sample-specific fragments by cell population. By default this is FALSE and sample-specific fragments are returned.</dd>


<dt>numCores</dt>
<dd>Number of cores to use.</dd>


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

</dl>

getPopFrags: Extract fragments by populations from an ArchR Project

Description

Usage

Value

Arguments