subsetMOCHAObject

<code>subsetMOCHAObject</code> subsets a tileResults-type object (from
 callOpenTiles), or a SummarizedExperiment-type object (from
 getSampleTileMatrix), either by cell type or sample metadata.

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

subsetMOCHAObject function

<dl><dt>Object</dt>
<dd>A MultiAssayExperiment or RangedSummarizedExperiment,</dd>
<dt>subsetBy</dt>
<dd>The variable to subset by. Can either be 'celltype', or a
column from the sample metadata (see `colData(Object)`).</dd>
<dt>groupList</dt>
<dd>the list of cell type names or sample-associated data that
should be used to subset the Object</dd>
<dt>removeNA</dt>
<dd>If TRUE, removes groups in groupList that are NA. If FALSE,
keep groups that are NA.</dd>
<dt>subsetPeaks</dt>
<dd>If `subsetBy` = 'celltype', subset the tile
set to tiles only called in those cell types. Default is TRUE.</dd>
<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd></dl>

Arguments

subsetMOCHAObject — subsetMOCHAObject

<dl>

<dt>Object</dt>
<dd>A MultiAssayExperiment or RangedSummarizedExperiment,</dd>


<dt>subsetBy</dt>
<dd>The variable to subset by. Can either be 'celltype', or a
column from the sample metadata (see `colData(Object)`).</dd>


<dt>groupList</dt>
<dd>the list of cell type names or sample-associated data that
should be used to subset the Object</dd>


<dt>removeNA</dt>
<dd>If TRUE, removes groups in groupList that are NA. If FALSE,
keep groups that are NA.</dd>


<dt>subsetPeaks</dt>
<dd>If `subsetBy` = 'celltype', subset the tile
set to tiles only called in those cell types. Default is TRUE.</dd>


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

</dl>

subsetMOCHAObject: `subsetMOCHAObject`

Description

Usage

Value

Arguments