phyloseq_adonis: Permutational multivariate analysis of variance using...

View source: R/phyloseq_adonis.R

phyloseq_adonisR Documentation

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.