Permanova: Permutational Multivariate Analysis of Variance along...

In nuriamw/micro4all: Microbiome for all

Permutational Multivariate Analysis of Variance along multiple distances metrics

Description

This function is a modification of adonis from vegan package. It performs PERMANOVA analysis looping along a list of distances metrics (Bray-Curtis, UniFrac, Weighted UniFrac...).

Usage

Permanova(data, formula, distances, type = "samples", adonis.options, ...)

Arguments

data	a phyloseq-class. For more details, check distance funtion.
formula	Model formula to be passed to adonis.
distances	Character string including multiple distance methods to be used. Further details to be found in distance.
type	character string with the type of comparison to used (sample-wise or taxa-wise, with default c("Samples")). Check distance for further details.
adonis.options	Further arguments to be passed to adonis. They should be included as a list (see examples)
...	Further arguments to be passed to distance function from package phyloseq.

Value

Returns a list with to elements:

1. A data frame containing the aov.tab component of resulting anova.cca from adonis for every distance used. This includes information of sources of variation, degrees of freedom, sequential sums of squares, mean squares, F statistics, partial R-squared and p-values, based on N permutations

2. A list with as many elements as distances were set. Each element includes all information provided by an typical anova.cca result object.

Examples

permanova_location<- Permanova(normalized_phyloseq,distances = c("bray",
"unifrac", "wunifrac"), formula = "location", adonis.options= list(Permutations=200))

nuriamw/micro4all documentation built on May 2, 2024, 9:18 a.m.