aldex.pvals: Calculate p-values adjusting for changes in sign as described...

In ALDEx3: Linear Models for Sequence Count Data

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

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)

Usage

aldex.pvals(p.lower, p.upper, p.adjust.method, onesided = FALSE)

Arguments

p.lower	A P x D x S matrix for P covariates, D taxa/genes, and S monte carlo samples representing the lower tail p.values
p.upper	A P x D x S matrix for P covariates, D taxa/genes, and S monte carlo samples representing the upper tail p.values
p.adjust.method	An adjutment method for p.adjust
onesided	(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.

Value

A list with P x D matrices with the non-adjusted and adjusted p-values.

Author(s)

Justin Silverman, Kyle McGovern

References

Nixon G, Gloor GB, Silverman JD (2025). "Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization". Genome Biology. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s13059-025-03609-3")}

ALDEx3 documentation built on Oct. 20, 2026, 1:07 a.m.