phyloseq_adonis: Permutational multivariate analysis of variance using...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Permutational multivariate analysis of variance using distance matrices (PERMANOVA) for phyloseq objects

Description

Permutational multivariate analysis of variance using distance matrices (PERMANOVA) for phyloseq objects

Usage

phyloseq_adonis(
  physeq,
  group.var = NULL,
  method = "bray",
  pairwise = FALSE,
  add_permdisp = TRUE,
  permut = 999,
  permdisp_type = "median",
  p.adj = "fdr",
  all_results = TRUE,
  comparison_sep = ".",
  ...
)

Arguments

physeq	A phyloseq-class object
group.var	Variable name (contained in sample_data) to test (RHS in adonis formula)
method	Distance/dissimilarity method (as character string; see distanceMethodList)
pairwise	Logical, perform pairwise adonis (dafault, FALSE)
add_permdisp	Logical; if TRUE (default), results of tests for homogeneity of multivariate dispersions will be added to output (see betadisper)
permut	Number of permutations required
permdisp_type	Use the spatial median (default) or the group centroid for the analysis for homogeneity of multivariate dispersions (see betadisper)
p.adj	Logical or character; if TRUE, adjust P-values for multiple comparisons with FDR; if character, specify correction method from p.adjust ("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", or "none")
all_results	Logical, return results of adonis and data subsets for each pairwise comparison
comparison_sep	Character string to separate the levels of independent variable the in the pairwise comparison names (default, ".")
...	Additional arguments will be passed to adonis and permutest

Details

Currently, only categorical variables (factors) are supported in 'group.var'.

Value

List with adonis and permdisp results

See Also

adonis, betadisper, adonis_pairwise

Examples

data("GlobalPatterns")
phyloseq_adonis(physeq = GlobalPatterns, group.var = "SampleType", all_results = FALSE, pairwise = TRUE, permut = 20)

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.