as.ChromatinAssay

as.ChromatinAssay.Assay

Convert objects to a ChromatinAssay

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

as.ChromatinAssay function

<dl><dt>x</dt>
<dd>An object to convert to class <code>ChromatinAssay</code></dd>
<dt>...</dt>
<dd>Arguments passed to other methods</dd>
<dt>ranges</dt>
<dd>A GRanges object</dd>
<dt>seqinfo</dt>
<dd>A <code>Seqinfo</code> object containing basic
information about the genome used. Alternatively, the name of a UCSC genome
can be provided and the sequence information will be downloaded from UCSC.</dd>
<dt>annotation</dt>
<dd>Genomic annotation. It must have the following columns:<ul>
<li>tx_id or transcript_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>motifs</dt>
<dd>A <code>Motif</code> object</dd>
<dt>fragments</dt>
<dd>A list of <code>Fragment</code> objects</dd>
<dt>bias</dt>
<dd>Tn5 integration bias matrix</dd>
<dt>positionEnrichment</dt>
<dd>A named list of position enrichment matrices.</dd>
<dt>sep</dt>
<dd>Characters used to separate the chromosome, start, and end
coordinates in the row names of the data matrix</dd></dl>

Arguments

Convert objects to a ChromatinAssay — as.ChromatinAssay

<dl>

<dt>x</dt>
<dd>An object to convert to class <code>ChromatinAssay</code></dd>


<dt>...</dt>
<dd>Arguments passed to other methods</dd>


<dt>ranges</dt>
<dd>A GRanges object</dd>


<dt>seqinfo</dt>
<dd>A <code>Seqinfo</code> object containing basic
information about the genome used. Alternatively, the name of a UCSC genome
can be provided and the sequence information will be downloaded from UCSC.</dd>


<dt>annotation</dt>
<dd>Genomic annotation. It must have the following columns:<ul>
<li>tx_id or transcript_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>motifs</dt>
<dd>A <code>Motif</code> object</dd>


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


<dt>bias</dt>
<dd>Tn5 integration bias matrix</dd>


<dt>positionEnrichment</dt>
<dd>A named list of position enrichment matrices.</dd>


<dt>sep</dt>
<dd>Characters used to separate the chromosome, start, and end
coordinates in the row names of the data matrix</dd>

</dl>

as.ChromatinAssay: Convert objects to a ChromatinAssay

Description

Usage

Arguments