PERMANOVA — perform_permanova • notame

Performs permutational multivariate analysis of variance. Uses package called PERMANOVA.

Usage

perform_permanova(
  object,
  group,
  all_features = FALSE,
  transform = "Standardize columns",
  coef = "Pythagorean",
  assay.type = NULL,
  ...
)

Arguments

object: a SummarizedExperiment or MetaboSet object
group: character, name of the column to compare
all_features: should all features be included?
transform: Transformation to use in IniTransform. By default uses "Standardize columns".
coef: Coefficient to calculate continuous distances in IniTransform. By default uses Pythagorean distances.
assay.type: character, assay to be used in case of multiple assays
...: other parameters to PERMANOVA

Value

A PERMANOVA object.

Examples

data(example_set)
permanova_res <- perform_permanova(drop_qcs(example_set), group = "Group")
#> INFO [2025-06-23 22:37:36] Starting PERMANOVA tests
#> INFO [2025-06-23 22:37:37] PERMANOVA performed