DepthCor

Compute the correlation between total counts and each reduced
dimension component.

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

DepthCor function

<dl><dt>object</dt>
<dd>A <code>Seurat</code> object</dd>
<dt>assay</dt>
<dd>Name of assay to use for sequencing depth. If NULL, use the
default assay.</dd>
<dt>reduction</dt>
<dd>Name of a dimension reduction stored in the
input object</dd>
<dt>n</dt>
<dd>Number of components to use. If <code>NULL</code>, use all components.</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code><a href="/link/cor?package=Signac&version=1.14.0" data-mini-rdoc="Signac::cor">cor</a></code></dd></dl>

Arguments

Plot sequencing depth correlation — DepthCor

<dl>

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


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


<dt>reduction</dt>
<dd>Name of a dimension reduction stored in the
input object</dd>


<dt>n</dt>
<dd>Number of components to use. If <code>NULL</code>, use all components.</dd>


<dt>...</dt>
<dd>Additional arguments passed to <code><a href='https://rdrr.io/r/stats/cor.html'>cor</a></code></dd>

</dl>

DepthCor: Plot sequencing depth correlation

Description

Usage

Value

Arguments

Examples