FRiP

Calculate fraction of reads in peaks per cell

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

FRiP function

<dl><dt>object</dt>
<dd>A Seurat object</dd>
<dt>assay</dt>
<dd>Name of the assay containing a peak x cell matrix</dd>
<dt>total.fragments</dt>
<dd>Name of a metadata column containing the total number
of sequenced fragments for each cell. This can be computed using the
<code>CountFragments</code> function.</dd>
<dt>col.name</dt>
<dd>Name of column in metadata to store the FRiP information.</dd>
<dt>verbose</dt>
<dd>Display messages</dd></dl>

Arguments

Calculate fraction of reads in peaks per cell — FRiP

<dl>

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


<dt>assay</dt>
<dd>Name of the assay containing a peak x cell matrix</dd>


<dt>total.fragments</dt>
<dd>Name of a metadata column containing the total number
of sequenced fragments for each cell. This can be computed using the
<code>CountFragments</code> function.</dd>


<dt>col.name</dt>
<dd>Name of column in metadata to store the FRiP information.</dd>


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

</dl>

FRiP: Calculate fraction of reads in peaks per cell

Description

Usage

Value

Arguments

Examples