summary.aldex

Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data.
Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) <doi:10.1186/s13059-025-03609-3> and McGovern et al. (2025) <doi:10.1101/2025.08.05.668734>.

Justin Silverman

ALDEx3

Linear Models for Sequence Count Data

Greg Gloor

Kyle McGovern

summary.aldex function

<dl><dt>object</dt>
<dd>An object of class <code>aldex</code></dd>
<dt>ignore.intercept</dt>
<dd>(default=TRUE), ignore intercept when creating
summary table</dd>
<dt>...</dt>
<dd>Additional arguments (currently ignored).</dd></dl>

Arguments

Author

Summary Method for ALDEx3 Objects — summary.aldex

<dl>

<dt>object</dt>
<dd>An object of class <code>aldex</code></dd>


<dt>ignore.intercept</dt>
<dd>(default=TRUE), ignore intercept when creating
summary table</dd>


<dt>...</dt>
<dd>Additional arguments (currently ignored).</dd>

</dl>

summary.aldex: Summary Method for ALDEx3 Objects

Description

Usage

Value

Arguments

Author

Details