permanova: Permanova between a otutab and a variable

In pctax: Professional Comprehensive Omics Data Analysis

Permanova between a otutab and a variable

Description

Permanova between a otutab and a variable

Usage

permanova(
  otutab,
  envs,
  norm = TRUE,
  each = TRUE,
  method = "adonis",
  dist = "bray",
  nperm = 999,
  ...
)

Arguments

otutab	an otutab data.frame, samples are columns, taxs are rows.
envs	factors need to test
norm	should normalize?(default:TRUE)
each	test factor one by one, rather than whole
method	adonis/mrpp/anosim/mantel
dist	if use pcoa or nmds, your can choose a dist method (default: bray)
nperm	numbers of permutations to perform
...	additional

Value

a g_test object with these columns

group	the test group or factor
r	relationship
r2	model R-square
p_value	model test p_value
sig	whether significant

References

https://blog.csdn.net/qq_42458954/article/details/110390488

Examples

data(otutab, package = "pcutils")
permanova(otutab, metadata[, c(2:10)]) -> adonis_res
print(adonis_res)
plot(adonis_res)

pctax documentation built on May 29, 2024, 10:03 a.m.