Run differential association tests between taxa counts and exogenous factors.

Run differential association tests between taxa counts and exogenous factors.

association(ps, variables = NULL, tax = "genus", confounders = NULL,
  min_count = 10, in_samples = 0.1, independent_weighting = TRUE,
  standardize = TRUE, shrink = TRUE)

Arguments

ps

A phyloseq object containing the taxa counts.
variables

Names of exogenous variables to include. Defaults to all variables.
tax

The taxa level on which to run differential tests. Defaults to genus.
confounders

A character vector containing the confounders that should be used.
min_count

Minimum required number of average counts for a taxa.
in_samples

Taxa must be present in at least this fraction of samples.
independent_weighting

Whether to adjust p values by independent weighting or normal Benjamini-Hochberg. factors.
standardize

Whether to standardize continuous variables to a mean of zero and a variance of 1. If True log fold changes for those variables denote are relative to a change of one standard deviation in the variable value.
shrink

Whether to return shrunken log fold changes. Defaults to true.

Value

A data.table containing the results.

Examples

 NULL
#> NULL