pctax (version 0.1.3)

permanova: 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,
  ...
)

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

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

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)