do_alpha_div_test {animalcules}R Documentation

Alpha diversity statistical test

Description

Alpha diversity statistical test

Usage

do_alpha_div_test(MAE, tax_level, condition,
  alpha_metric = c("inverse_simpson", "gini_simpson", "shannon",
  "fisher", "coverage"), alpha_stat = c("Wilcoxon rank sum test",
  "T-test", "Kruskal-Wallis"))

Arguments

MAE

A multi-assay experiment object

tax_level

The taxon level used for organisms

condition

Which condition to group samples

alpha_metric

Which alpha diversity metric to use

alpha_stat

Which stat test to use

Value

A dataframe

Examples

data_dir = system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
p <- do_alpha_div_test(toy_data,
                       tax_level = "genus",
                       condition = "DISEASE",
                       alpha_metric = "shannon",
                       alpha_stat = "Wilcoxon rank sum test")
p


[Package animalcules version 1.0.3 Index]