AddChromatinModule

Compute chromVAR deviations for groups of peaks. The goal of this function is
similar to that of <code>AddModuleScore</code> except that it is
designed for single-cell chromatin data. The chromVAR deviations for each
group of peaks will be added to the object metadata.

A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Tim Stuart

Signac

Analysis of Single-Cell Chromatin Data

Avi Srivastava

Paul Hoffman

Rahul Satija

AddChromatinModule function

<dl><dt>object</dt>
<dd>A Seurat object</dd>
<dt>features</dt>
<dd>A named list of features to include in each module. The name
of each element in the list will be used to name the modules computed, which
will be stored in the object metadata.</dd>
<dt>genome</dt>
<dd>A BSgenome object</dd>
<dt>assay</dt>
<dd>Name of assay to use. If NULL, use the default assay.</dd>
<dt>verbose</dt>
<dd>Display messages</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code>RunChromVAR</code></dd></dl>

Arguments

Add chromatin module — AddChromatinModule

<dl>

<dt>object</dt>
<dd>A Seurat object</dd>


<dt>features</dt>
<dd>A named list of features to include in each module. The name
of each element in the list will be used to name the modules computed, which
will be stored in the object metadata.</dd>


<dt>genome</dt>
<dd>A BSgenome object</dd>


<dt>assay</dt>
<dd>Name of assay to use. If NULL, use the default assay.</dd>


<dt>verbose</dt>
<dd>Display messages</dd>


<dt>...</dt>
<dd>Additional arguments passed to <code>RunChromVAR</code></dd>

</dl>

AddChromatinModule: Add chromatin module

Description

Usage

Value

Arguments