PERMANOVA_R2: PERMANOVA R2 of batch and variable of interest

In wdl2459/ConQuR: Batch Effects Removal for Microbiome Data in Large-Scale Epidemiology Studies via Conditional Quantile Regression

PERMANOVA R2 of batch and variable of interest

Description

PERMANOVA R2 of batch and variable of interest

Usage

PERMANOVA_R2(TAX, batchid, covariates, key_index)

Arguments

TAX	The taxa read count table, samples (row) by taxa (col).
batchid	The batch indicator, must be a factor.
covariates	The data.frame contains the key variable of interest and other covariates.
key_index	An integer, location of the variable of interest in covariates.

Details

Three PERMANOVA R2 will be computed: (1) the standard one (adnois), (2) on euclidified dissimilarities (adonis2, sqrt.dist=T), and (3) with a constant added to the non-diagonal dissimilarities such that all eigenvalues are non-negative in the underlying PCoA (adonis2, add=T).

Value

A list

• tab_count - A table summarizing PERMANOVA R2 computed on the original taxa read count table in Bray-Curtis dissimilarity.

• tab_rel - A table summarizing PERMANOVA R2 computed on the corresponding relative abundance table in Euclidean dissimilarity (Aitchison dissimilarity).

References

• Anderson, M. J. (2014). Permutational multivariate analysis of variance (PERMANOVA). Wiley statsref: statistics reference online, 1-15.

wdl2459/ConQuR documentation built on Aug. 28, 2022, 6:08 a.m.