VariantPlot

Plot the Pearson correlation between allele frequencies on each strand
versus the log10 mean-variance ratio for the allele.

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

VariantPlot function

<dl><dt>variants</dt>
<dd>A dataframe containing variant information. This should be
computed using <code>IdentifyVariants</code></dd>
<dt>min.cells</dt>
<dd>Minimum number of high-confidence cells detected with the
variant for the variant to be displayed.</dd>
<dt>concordance.threshold</dt>
<dd>Strand concordance threshold</dd>
<dt>vmr.threshold</dt>
<dd>Mean-variance ratio threshold</dd></dl>

Arguments

Plot strand concordance vs. VMR — VariantPlot

<dl>

<dt>variants</dt>
<dd>A dataframe containing variant information. This should be
computed using <code>IdentifyVariants</code></dd>


<dt>min.cells</dt>
<dd>Minimum number of high-confidence cells detected with the
variant for the variant to be displayed.</dd>


<dt>concordance.threshold</dt>
<dd>Strand concordance threshold</dd>


<dt>vmr.threshold</dt>
<dd>Mean-variance ratio threshold</dd>

</dl>

VariantPlot: Plot strand concordance vs. VMR

Description

Usage

Arguments