do_alpha_div_test {animalcules} | R Documentation |
Alpha diversity statistical test
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"))
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 |
A dataframe
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