diversity_beta_test {animalcules}R Documentation

Beta diversity test (by default we use bray-curtis distance)

Description

Beta diversity test (by default we use bray-curtis distance)

Usage

diversity_beta_test(MAE, tax_level, input_beta_method,
  input_select_beta_condition, input_select_beta_stat_method,
  input_num_permutation_permanova = 999)

Arguments

MAE

A multi-assay experiment object

tax_level

The taxon level used for organisms

input_beta_method

bray, jaccard

input_select_beta_condition

Which condition to group samples

input_select_beta_stat_method

PERMANOVA,Kruskal-Wallis,Wilcoxon test

input_num_permutation_permanova

number of permutations

Value

A plotly object

Examples

data_dir = system.file('extdata/MAE.rds', package = 'animalcules')
toy_data <- readRDS(data_dir)
p <- diversity_beta_test(toy_data,
                         tax_level = 'genus',
                         input_beta_method = 'bray',
                         input_select_beta_condition = 'DISEASE',
                         input_select_beta_stat_method = 'PERMANOVA',
                         input_num_permutation_permanova = 999)
p


[Package animalcules version 1.0.3 Index]