permute_rho: Permutes the pair-wise Spearman rank co-occurrence, to...

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

Permutes the pair-wise Spearman rank co-occurrence, to determine a significant rho-cutoff. Function from the phylosmith-package.

Description

Permutes the pair-wise Spearman rank co-occurrence, to determine a significant rho-cutoff.

Usage

permute_rho(phyloseq_obj, treatment = NULL, subset = NULL,
replicate_samples = NULL, permutations = 10, method = 'spearman',
cores = 1)

Arguments

phyloseq_obj	A phyloseq-class object.
treatment	Column name as a string or numeric in the sample_data. This can be a vector of multiple columns and they will be combined into a new column.
subset	A factor within the treatment. This will remove any samples that to not contain this factor. This can be a vector of multiple factors to subset on.
replicate_samples	Column name as a string or numeric in the sample_data that indicates which samples are non-independent of each other.
permutations	numeric Number of iterations to compute.
method	Which correlation method to calculate, "pearson", "spearman".
cores	numeric Number of CPU cores to use for the pair-wise permutations. Default (0) uses max cores available. Parallelization not available for systems running MacOS without openMP configuration.

Value

table

See Also

co_occurrence

Examples

permute_rho(soil_column, treatment = c('Matrix', 'Treatment'),
subset = 'Amended', replicate_samples = 'Day', permutations = 1,  cores = 0)

schuyler-smith/phyloschuyler documentation built on Aug. 16, 2024, 5:36 a.m.