AccessiblePeaks

Find accessible peaks in a set of cells

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

AccessiblePeaks function

<dl><dt>object</dt>
<dd>A Seurat object</dd>
<dt>assay</dt>
<dd>Name of assay to use</dd>
<dt>idents</dt>
<dd>A set of identity classes to find accessible peaks for</dd>
<dt>cells</dt>
<dd>A vector of cells to find accessible peaks for</dd>
<dt>min.cells</dt>
<dd>Minimum number of cells with the peak accessible (&gt;0 counts)
for the peak to be called accessible</dd></dl>

Arguments

Accessible peaks — AccessiblePeaks

<dl>

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


<dt>assay</dt>
<dd>Name of assay to use</dd>


<dt>idents</dt>
<dd>A set of identity classes to find accessible peaks for</dd>


<dt>cells</dt>
<dd>A vector of cells to find accessible peaks for</dd>


<dt>min.cells</dt>
<dd>Minimum number of cells with the peak accessible (&gt;0 counts)
for the peak to be called accessible</dd>

</dl>

AccessiblePeaks: Accessible peaks

Description

Usage

Value

Arguments