aldex.pvals

Calculate p-values adjusting for changes in sign as described by Nixon
et al. (2024) in Beyond Normalization: Incorporating Scale Uncertainty
in Microbiome and Gene Expression Analysis (internal only)

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.pvals function

<dl><dt>p.lower</dt>
<dd>A P x D x S matrix for P covariates, D taxa/genes, and S
monte carlo samples representing the lower tail p.values</dd>
<dt>p.upper</dt>
<dd>A P x D x S matrix for P covariates, D taxa/genes, and S
monte carlo samples representing the upper tail p.values</dd>
<dt>p.adjust.method</dt>
<dd>An adjutment method for p.adjust</dd>
<dt>onesided</dt>
<dd>(default: FALSE) if sided return p-values for two-sided
test. Otherwise if "lower" or "upper" return one-sided test corresponding
to test that estimate is negative or positive respectively.</dd></dl>

Arguments

Author

Calculate p-values adjusting for changes in sign as described by Nixon
et al. (2024) in Beyond Normalization: Incorporating Scale Uncertainty
in Microbiome and Gene Expression Analysis (internal only) — aldex.pvals

<dl>

<dt>p.lower</dt>
<dd>A P x D x S matrix for P covariates, D taxa/genes, and S
monte carlo samples representing the lower tail p.values</dd>


<dt>p.upper</dt>
<dd>A P x D x S matrix for P covariates, D taxa/genes, and S
monte carlo samples representing the upper tail p.values</dd>


<dt>p.adjust.method</dt>
<dd>An adjutment method for p.adjust</dd>


<dt>onesided</dt>
<dd>(default: FALSE) if sided return p-values for two-sided
test. Otherwise if "lower" or "upper" return one-sided test corresponding
to test that estimate is negative or positive respectively.</dd>

</dl>

Calculate p-values adjusting for changes in sign as described by Nixon
et al. (2024) in Beyond Normalization: Incorporating Scale Uncertainty
in Microbiome and Gene Expression Analysis (internal only)

aldex.pvals: Calculate p-values adjusting for changes in sign as described by Nixon et al. (2024) in Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis (internal only)

Description

Usage

Value

Arguments

Author

References