variable_correlation: Computes the correlation of numerical variables with taxa...

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

Computes the correlation of numerical variables with taxa Function from the phylosmith-package.

Description

Computes the correlation of numerical variables with taxa

Usage

variable_correlation(phyloseq_obj, variables, treatment = NULL,
 subset = NULL, classification = NULL, method = "spearman", cores = 1)

Arguments

phyloseq_obj	A phyloseq-class object.
variables	Numericla factors within the in the sample_data to correlate with the abundance data.
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.
classification	Column name as a string or numeric in the tax_table for the factor to conglomerate by.
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

data.table

See Also

permute_rho phylosmith

Examples

variable_correlation(soil_column, variables = "Day",
treatment = c("Matrix", "Treatment"), subset = "Amended",
classification = "Phylum", method = "spearman", cores = 1)

schuyler-smith/phyloschuyler documentation built on Feb. 5, 2025, 12:14 p.m.