Perform PERMANOVA and pairwise comparisons — permanova

This function performs PERMANOVA on the given data and metadata, with options for filtering groups. It also conducts post-hoc pairwise comparisons and adjusts p-values for multiple testing. The function returns the PERMANOVA results, raw pairwise comparison results, and matrices of adjusted p-values, F values, and R square for pairwise comparisons

Usage

permanova_stat(
  data,
  metadata,
  mode,
  filter_group = FALSE,
  group_list = NULL,
  permutations = 5000
)

Arguments

data: A data frame or distance matrix for PERMANOVA
metadata: A data frame containing sample metadata, including a 'group' column
mode: The mode of the input data: 'data' for raw data or 'distance' for a distance matrix
filter_group: Boolean to filter groups based on a provided list (default: FALSE)
group_list: A vector of group names to filter (default: NULL)
permutations: The number of permutations for the PERMANOVA test (default: 5000)

Value

A list containing the PERMANOVA results, raw pairwise comparison results, and matrices of adjusted p-values, F values, and R square for pairwise comparisons

Examples

if (FALSE) {
permanova_results <- permanova_stat(
 data = feature_data, metadata = mmo$metadata, 
 mode = 'data', filter_group = TRUE, group_list = c("Control", "Treatment1"), 
 permutations = 5000
)
permanova_results <- permanova_stat(
 data = betadiv, metadata = mmo$metadata, 
 mode = 'distance', permutations = 10000
)
}