do_alpha_div_test: Alpha diversity statistical test

In animalcules: Interactive microbiome analysis toolkit

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

animalcules documentation built on Nov. 8, 2020, 6:47 p.m.