permanova: Perform a PERMANOVA analysis for group differences of a...

In CenterForStatistics-UGent/RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Perform a PERMANOVA analysis for group differences of a predefined cofactor using the pseudo F-statistic

Description

Perform a PERMANOVA analysis for group differences of a predefined cofactor using the pseudo F-statistic

Usage

permanova(
  rcmObj,
  groups,
  nPerm = 10000,
  Dim = seq_len(rcmObj$k),
  verbose = TRUE
)

Arguments

rcmObj	an RCM object
groups	a factor of length n with cluster memberships, or a name of a variable contained in the RCM object
nPerm	Number of permutations in the PERMANOVA
Dim	Dimensions on which the test should be performed. Defaults to all dimensions of the fitted RCM object.
verbose	a boolean, should output be printed?

Value

A list with components

statistic	The pseudo F-statistic
p.value	The p-value of the PERMANOVA

See Also

RCM

Examples

data(Zeller)
require(phyloseq)
tmpPhy = prune_taxa(taxa_names(Zeller)[1:100],
prune_samples(sample_names(Zeller)[1:50], Zeller))
zellerRCM = RCM(tmpPhy, round = TRUE)
zellerPermanova = permanova(zellerRCM, "Diagnosis")

CenterForStatistics-UGent/RCM documentation built on April 24, 2023, 8:26 p.m.