R/testing.R
combinatorial_association.Rd
Run differential association tests between between all combinations of a factor variable with DESeq2. Can be used as post-hoc test for regression.
combinatorial_association(
ps,
variable,
tax = "genus",
confounders = NULL,
min_abundance = 10,
in_samples = 0.1,
independent_weighting = TRUE,
standardize = TRUE,
shrink = TRUE
)
A phyloseq object containing the taxa counts.
The factor variable to permute.
The taxa level on which to run differential tests. Defaults to genus.
A character vector containing the confounders that should be used.
Minimum required number of average counts for a taxa.
Taxa must be present in at least this fraction of samples.
Whether to adjust p values by independent weighting or normal Benjamini-Hochberg. factors.
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.
Whether to return shrunken log fold changes. Defaults to true.
A data.table containing the results.
NULL
#> NULL