doKruskalWallisTest: Do Kruskal-Wallis Test Taxa and Multiple Groups

In RIVM-IIV-Microbiome/biomeStats: Methods for carrying out association studies of the microbiome

Do Kruskal-Wallis Test Taxa and Multiple Groups

Description

Do Kruskal-Wallis Test Taxa and Multiple Groups

Usage

doKruskalWallisTest(
  x,
  sample_group = NULL,
  adj_method = "BH",
  effect_size = TRUE,
  ...
)

Arguments

x	A phyloseq object
sample_group	Variable in sample_data to test for differences in taxa abundances
adj_method	One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default="BH". For more information see adjust_pvalue
effect_size	Logical. Default is TRUE. Calculates effect size for Kruskal-Wallis test using kruskal_effsize
...	Additional parameters that are passed on to kruskal_effsize

Details

Performs Kruskal-Wallis Test one or multiple levels and is a wrapper using kruskal_test, adjust_pvalue and add_significance for an input phyloseq object. Useful for comparing large number of taxa between groups.

Value

A tibble.

Author(s)

Sudarshan A. Shetty

See Also

kruskal_test kruskal_effsize

Examples

library(biomeStats)
library(phyloseq)
library(microbiome)
library(dplyr)
data("FuentesIliGutData")
ps.rel <- microbiome::transform(FuentesIliGutData, "compositional")
ps.rel <- core(ps.rel, detection=0.001, prevalence=50/100)

kw_results <- doKruskalWallisTest(ps.rel,
                                  sample_group = "ILI",
                                  adj_method = "BH",
                                  effect_size = TRUE)

print(kw_results)

RIVM-IIV-Microbiome/biomeStats documentation built on Sept. 14, 2022, 5:15 p.m.