pnova: PERMANOVA Analysis

In microresearcher/MicroVis: Microbiome Analysis and Visualization

PERMANOVA Analysis

Description

PERMANOVA Analysis

Usage

pnova(
  dataset = NULL,
  dist = "bray",
  weighted = F,
  allFactors = T,
  factors = NULL,
  alpha = 0.05
)

Arguments

dataset	MicroVis dataset. Defaults to active dataset
dist	Method for dissimilarity calculation. One of either "bray", "euclidean", "jaccard", "unifrac", "manhattan", "canberra", "clark", "kulczynski", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao", "mahalanobis", "chisq" or "chord"
weighted	(Optional) If method is set to "unifrac", whether to perform weighted or unweighted unifrac. Defaults to FALSE
allFactors	Perform PERMANOVA analysis on all factors? Defaults to TRUE if no factors are specified (below)
factors	(Optional) Specify factors to perform PERMANOVA on. If none are specified, then all factors will be included
alpha	Significance threshold for PERMANOVA results before performing PERMDISP analysis. Defaults to 0.05

Value

PERMANOVA and PERMDISP results

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.