combinatorial_association: Run differential association tests between between all...

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Run differential association tests between between all combinations of a factor variable with DESeq2. Can be used as post-hoc test for regression.

Description

Run differential association tests between between all combinations of a factor variable with DESeq2. Can be used as post-hoc test for regression.

Usage

combinatorial_association(
  ps,
  variable,
  tax = "genus",
  confounders = NULL,
  min_abundance = 10,
  in_samples = 0.1,
  independent_weighting = TRUE,
  standardize = TRUE,
  shrink = TRUE
)

Arguments

ps	A phyloseq object containing the taxa counts.
variable	The factor variable to permute.
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_abundance	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

Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.