permanova: PERMANOVA

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

Evaluate whether the group(s) has a significant effect on overall gut microbiota composition.

Usage

permanova(obj, distance_method = "bray", group = "TreatmentGroup")

Arguments

obj	An object to be converted to a taxmap object with create_taxmap.
distance_method	Use a desired distance method, Default: 'bray'
group	The group or column in the metadata to test upon, Default: 'TreatmentGroup'

Value

Returns a list which includes permanova, anova, coefficients, and top coefficients.

See Also

View top_coefficients_barplot to plot the top_coefficients returned from this function. See adonis and betadisper to understand more about how the permanova data was generated

Examples

## Not run: 
if (interactive()) {
  library(MicrobiomeR)
  data <- analyzed_silva
  p <- permanova(obj = data, group = "TreatmentGroup")
  p$permanova
}

## End(Not run)

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.