aldex.lm.sim.clr

Not designed to create realistic data. Does not add any noise to linear
regression! True W is in CLR Corrdinates

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

aldex.lm.sim.clr function

<dl><dt>D</dt>
<dd>number of taxa/genes</dd>
<dt>N</dt>
<dd>number of samples</dd>
<dt>P</dt>
<dd>number of covariates</dd>
<dt>depth</dt>
<dd>sum of counts for each multinomial draw</dd></dl>

Arguments

Author

Simulation function soley for testing and exploring ALDEx3, Truth is in CLR
Coordinates. — aldex.lm.sim.clr

<dl>

<dt>D</dt>
<dd>number of taxa/genes</dd>


<dt>N</dt>
<dd>number of samples</dd>


<dt>P</dt>
<dd>number of covariates</dd>


<dt>depth</dt>
<dd>sum of counts for each multinomial draw</dd>

</dl>

aldex.lm.sim.clr: Simulation function soley for testing and exploring ALDEx3, Truth is in CLR Coordinates.

Description

Usage

Value

Arguments

Author