pilotLMEM

`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>pilotLMEM</code> Runs linear mixed-effects modeling for
 continuous, non-zero inflated data using <code>lmer</code>

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

pilotLMEM function

<dl><dt>ExperimentObj</dt>
<dd>A SummarizedExperiment-type object generated from
chromVAR, makePseudobulkRNA, or other. Objects from getSampleTileMatrix can work,
but we recommend runZIGLMM for those objects, not runLMEM&gt;</dd>
<dt>assayName</dt>
<dd>a character string, matching the name of an assay within the SummarizedExperiment.
The assay named will be used for modeling.</dd>
<dt>modelFormula</dt>
<dd>The formula to use with lmerTest::lmer, in the
format (exp ~ factors). All factors must be found in column names
of the ExperimentObj metadata.</dd>
<dt>pilotIndices</dt>
<dd>A vector of integers defining the subset of
the ExperimentObj matrix. Default is 1:10.</dd>
<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd></dl>

Arguments

Execute a pilot run of single linear model on a subset of data — pilotLMEM

<dl>

<dt>ExperimentObj</dt>
<dd>A SummarizedExperiment-type object generated from
chromVAR, makePseudobulkRNA, or other. Objects from getSampleTileMatrix can work,
but we recommend runZIGLMM for those objects, not runLMEM&gt;</dd>


<dt>assayName</dt>
<dd>a character string, matching the name of an assay within the SummarizedExperiment.
The assay named will be used for modeling.</dd>


<dt>modelFormula</dt>
<dd>The formula to use with lmerTest::lmer, in the
format (exp ~ factors). All factors must be found in column names
of the ExperimentObj metadata.</dd>


<dt>pilotIndices</dt>
<dd>A vector of integers defining the subset of
the ExperimentObj matrix. Default is 1:10.</dd>


<dt>verbose</dt>
<dd>Set TRUE to display additional messages. Default is FALSE.</dd>

</dl>

pilotLMEM: Execute a pilot run of single linear model on a subset of data

Description

Usage

Value

Arguments