Motif-class

Motif

The Motif class is designed to store DNA sequence motif information,
including motif PWMs or PFMs, motif positions, and metadata.

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

Motif-class function

<dl>
<dt><code>data</code></dt>
<dd>A sparse, binary, feature x motif matrix. Columns
correspond to motif IDs, rows correspond to genomic features
(peaks or bins). Entries in the matrix should be 1 if the
genomic feature contains the motif, and 0 otherwise.</dd></dl>
<dt><code>pwm</code></dt>
<dd>A named list of position weight matrices</dd>
<dt><code>motif.names</code></dt>
<dd>A list containing the name of each motif</dd>
<dt><code>positions</code></dt>
<dd>A <code>GRangesList</code> object containing
exact positions of each motif.</dd>
<dt><code>meta.data</code></dt>
<dd>A dataframe for storage of additional
information related to each motif. This could include the
names of proteins that bind the motif.</dd>

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The Motif class — Motif-class

<dl>
<dt><code>data</code></dt>
<dd>A sparse, binary, feature x motif matrix. Columns
correspond to motif IDs, rows correspond to genomic features
(peaks or bins). Entries in the matrix should be 1 if the
genomic feature contains the motif, and 0 otherwise.</dd>


<dt><code>pwm</code></dt>
<dd>A named list of position weight matrices</dd>


<dt><code>motif.names</code></dt>
<dd>A list containing the name of each motif</dd>


<dt><code>positions</code></dt>
<dd>A <code>GRangesList</code> object containing
exact positions of each motif.</dd>


<dt><code>meta.data</code></dt>
<dd>A dataframe for storage of additional
information related to each motif. This could include the
names of proteins that bind the motif.</dd>


</dl>

Motif-class: The Motif class

Description

Arguments

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