getModelValues

`r lifecycle::badge("deprecated")`
 This function is deprecated - improved modeling functions can be found in 
 the package "ChAI" at https://github.com/aifimmunology/ChAI
 <code>getModelValues</code> Pull out a data.frame of model values (slope, significance, and std.error) for a given factor from the SummarizedExperiment output of runZIGLMM.

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

getModelValues function

<dl><dt>object</dt>
<dd>A SummarizedExperiment object generated from runZIGLMM.</dd>
<dt>specificVariable</dt>
<dd>A string, describing the factor of influence.</dd></dl>

Arguments

getModelValues from runZIGLMM output. — getModelValues

<dl>

<dt>object</dt>
<dd>A SummarizedExperiment object generated from runZIGLMM.</dd>


<dt>specificVariable</dt>
<dd>A string, describing the factor of influence.</dd>

</dl>

getModelValues: getModelValues from runZIGLMM output.

Description

Usage

Value

Arguments

Examples