Alpha diversity statistical test — do_alpha_div_test • animalcules

Alpha diversity statistical test

do_alpha_div_test(
  MAE,
  tax_level,
  condition,
  alpha_metric = c("inverse_simpson", "gini_simpson", "shannon", "fisher", "coverage",
    "unit"),
  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
#>         Wilcoxon rank sum exact test Welch Two Sample t-test
#> P-value                    0.3267236               0.4235008