ChromatinAssay-class

ChromatinAssay

The ChromatinAssay object is an extended <code>Assay</code>
for the storage and analysis of single-cell chromatin data.

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

ChromatinAssay-class function

<dl>
<dt><code>ranges</code></dt>
<dd>A <code>GRanges</code> object describing the
genomic location of features in the object</dd></dl>
<dt><code>motifs</code></dt>
<dd>A <code>Motif</code> object</dd>
<dt><code>fragments</code></dt>
<dd>A list of <code>Fragment</code> objects.</dd>
<dt><code>seqinfo</code></dt>
<dd>A <code>Seqinfo</code> object containing basic
information about the genome sequence used.</dd>
<dt><code>annotation</code></dt>
<dd>A <code>GRanges</code> object containing
genomic annotations. This should be a GRanges object with the following 
columns:<ul>
<li>tx_id: Transcript ID</li>
<li>gene_name: Gene name</li>
<li>gene_id: Gene ID</li>
<li>gene_biotype: Gene biotype (e.g. "protein_coding", "lincRNA")</li>
<li>type: Annotation type (e.g. "exon", "gap")</li>
</ul></dd>
<dt><code>bias</code></dt>
<dd>A vector containing Tn5 integration bias information
(frequency of Tn5 integration at different kmers)</dd>
<dt><code>positionEnrichment</code></dt>
<dd>A named list of matrices containing positional
enrichment scores for Tn5 integration (for example, enrichment at the TSS)</dd>
<dt><code>links</code></dt>
<dd>A <code>GRanges</code> object describing linked
genomic positions, such as co-accessible sites or enhancer-gene regulatory
relationships. This should be a <code>GRanges</code> object, where the start and
end coordinates are the two linked genomic positions, and must contain a
"score" metadata column.</dd>

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The ChromatinAssay class — ChromatinAssay-class

<dl>
<dt><code>ranges</code></dt>
<dd>A <code>GRanges</code> object describing the
genomic location of features in the object</dd>


<dt><code>motifs</code></dt>
<dd>A <code>Motif</code> object</dd>


<dt><code>fragments</code></dt>
<dd>A list of <code>Fragment</code> objects.</dd>


<dt><code>seqinfo</code></dt>
<dd>A <code>Seqinfo</code> object containing basic
information about the genome sequence used.</dd>


<dt><code>annotation</code></dt>
<dd>A <code>GRanges</code> object containing
genomic annotations. This should be a GRanges object with the following 
columns:<ul>
<li>tx_id: Transcript ID</li>
<li>gene_name: Gene name</li>
<li>gene_id: Gene ID</li>
<li>gene_biotype: Gene biotype (e.g. "protein_coding", "lincRNA")</li>
<li>type: Annotation type (e.g. "exon", "gap")</li>
</ul></dd>


<dt><code>bias</code></dt>
<dd>A vector containing Tn5 integration bias information
(frequency of Tn5 integration at different kmers)</dd>


<dt><code>positionEnrichment</code></dt>
<dd>A named list of matrices containing positional
enrichment scores for Tn5 integration (for example, enrichment at the TSS)</dd>


<dt><code>links</code></dt>
<dd>A <code>GRanges</code> object describing linked
genomic positions, such as co-accessible sites or enhancer-gene regulatory
relationships. This should be a <code>GRanges</code> object, where the start and
end coordinates are the two linked genomic positions, and must contain a
"score" metadata column.</dd>


</dl>

ChromatinAssay-class: The ChromatinAssay class

Description

Arguments

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