quantile_permuted_rhos: Calculate quantiles for the permuted rho values from the...

In schuyler-smith/phylosmith: Functions to help analyze data as phyloseq objects

Calculate quantiles for the permuted rho values from the Spearman-rank co-occurrence. Function from the phylosmith-package.

Description

Calculate quantiles for the permuted rho values from the Spearman-rank co-occurrence.

Usage

quantile_permuted_rhos(permuted_rhos, p = 0.05, by_treatment = TRUE)

Arguments

permuted_rhos	A data.table output from permute_rho.
p	The significance threshold for setting cutoffs.
by_treatment	Whether to find the rho cutoffs for each treatment individually or for the entire experiment. Suggested to do by treatment first, to see if there is any treatments that are outliers.

Value

data.frame

See Also

permute_rho

Examples

permuted_rhos <- permute_rho(soil_column,
treatment = c('Matrix', 'Treatment'), replicate_samples = 'Day',
permutations = 1,  cores = 0)
quantile_permuted_rhos(permuted_rhos)
quantile_permuted_rhos(permuted_rhos, by_treatment = FALSE)

schuyler-smith/phylosmith documentation built on Aug. 17, 2024, 10:19 a.m.