add_codifab: Perform compositional differential abundance analysis

In SWittouck/tidyamplicons: Functions to Manipulate and Visualize Amplicon Abundance Data

Perform compositional differential abundance analysis

Description

This function performs a differential abundance test for all pairwise ratios between taxa.

Usage

add_codifab(ta, condition, conditions = NULL, max_taxa = 30)

Arguments

ta	A tidyamplicons object
condition	A binary variable in the sample table (unquoted)
conditions	A character vector with exactly two categories of the condition variable
max_taxa	The maximum number of taxa to use

Details

A table called taxon_pairs will be added to the tidyamplicons object, with for each pair of a taxon and a reference taxon, the differential abundance of the taxon between the two conditions (with respect to the reference taxon). The test that is performed is a Wilcoxon rank sum test and the test statistic that is reported is the two-sample Hodges–Lehmann estimator (the median of all pairwise differences between the samples).

It is possible to supply the conditions to compare through the conditions argument. Other conditions than the two supplied will be removed from the data.

Value

A tidyamplicons object with an extra table taxon_pairs

SWittouck/tidyamplicons documentation built on Aug. 15, 2023, 3:14 a.m.