MotifCounts

Count the number of sequenced DNA fragments in a region surrounding each 
instance of a given DNA sequence motif.

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

MotifCounts function

<dl><dt>object</dt>
<dd>A Seurat object</dd>
<dt>motifs</dt>
<dd>A list of DNA sequence motif names. One matrix will be generated
for each motif</dd>
<dt>flanking.region</dt>
<dd>Amount of sequence to include surrounding the motif
itself</dd>
<dt>assay</dt>
<dd>Name of assay to use. Must be a ChromatinAssay</dd>
<dt>verbose</dt>
<dd>Display messages</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code>FeatureMatrix</code></dd></dl>

Arguments

Count fragments surrounding motif sites — MotifCounts

<dl>

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


<dt>motifs</dt>
<dd>A list of DNA sequence motif names. One matrix will be generated
for each motif</dd>


<dt>flanking.region</dt>
<dd>Amount of sequence to include surrounding the motif
itself</dd>


<dt>assay</dt>
<dd>Name of assay to use. Must be a ChromatinAssay</dd>


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


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

</dl>

MotifCounts: Count fragments surrounding motif sites

Description

Usage

Value

Arguments