MotifEnrichment

Test for enrichment of motifs within Group1 against a background
 Group2 using a hypergeometric t-test.

A statistical framework and analysis tool for open chromatin
analysis designed specifically for single cell ATAC-seq (Assay for
Transposase-Accessible Chromatin) data, after cell type/cluster
identification. These novel modules remove unwanted technical variation,
identify open chromatin, robustly models repeated measures in single cell
data, implement advanced statistical frameworks to model zero-inflation for
differential and co-accessibility analyses, and integrate with existing
databases and modules for downstream analyses to reveal biological insights.
MOCHA provides a statistical foundation for complex downstream analysis to
help advance the potential of single cell ATAC-seq for applied studies.
Methods for zero-inflated statistics are as described in:
Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>.
Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated
Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Imran McGrath

MOCHA

Modeling for Single-Cell Open Chromatin Analysis

Samir Rachid Zaim

Mark-Phillip Pebworth

Lauren Okada

Xiaojun Li

MotifEnrichment function

<dl><dt>Group1</dt>
<dd>A GRanges object, such as a set of significant differential
tiles.</dd>
<dt>Group2</dt>
<dd>A GRanges object containing background regions, non-overlapping
with Group1</dd>
<dt>motifPosList</dt>
<dd>A GRangesList of motifs and positions for each motif.
Must be named for each motif.</dd>
<dt>type</dt>
<dd>Optional, name of a metadata column in Group1 and Group2 to test
for enrichment the number of unique entries in column given by 'type'.
Default is NULL, which tests the number of Ranges.</dd></dl>

Arguments

MotifEnrichment — MotifEnrichment

<dl>

<dt>Group1</dt>
<dd>A GRanges object, such as a set of significant differential
tiles.</dd>


<dt>Group2</dt>
<dd>A GRanges object containing background regions, non-overlapping
with Group1</dd>


<dt>motifPosList</dt>
<dd>A GRangesList of motifs and positions for each motif.
Must be named for each motif.</dd>


<dt>type</dt>
<dd>Optional, name of a metadata column in Group1 and Group2 to test
for enrichment the number of unique entries in column given by 'type'.
Default is NULL, which tests the number of Ranges.</dd>

</dl>

MotifEnrichment: `MotifEnrichment`

Description

Usage

Value

Arguments