Calculate Microbe-Metabolite Correlations

Usage

calculate_correlation(
  object = NULL,
  microbiome_data = NULL,
  metabolome_data = NULL,
  sample_link = NULL,
  microbiome_rank = "Genus",
  microbiome_transform = c("relative", "log", "presence_absence", "clr", "none"),
  metabolome_transform = c("log", "none"),
  method = c("spearman", "pearson", "sparcc"),
  p_adjust_method = "BH",
  min_taxa_prevalence = 0,
  min_taxa_abundance = 0,
  min_metabolite_prevalence = 0,
  min_metabolite_sd = 0
)

calculate_correlation_spearman(...)

calculate_correlation_pearson(...)

calculate_correlation_sparcc(...)

Arguments

object

A microbiome_metabolome_dataset object.

microbiome_data

A microbiome_dataset object. Used when object is not supplied.

metabolome_data

A mass_dataset object. Used when object is not supplied.

sample_link

Optional sample link table used when object is not supplied.

microbiome_rank

Taxonomy rank for microbiome aggregation.

microbiome_transform

Microbiome transformation method.

metabolome_transform

Metabolome transformation method.

method

Correlation method.

p_adjust_method

Multiple-testing correction method.

min_taxa_prevalence

Minimum number of non-zero samples required for a microbiome feature.

min_taxa_abundance

Minimum mean abundance required for a microbiome feature.

min_metabolite_prevalence

Minimum number of non-zero samples required for a metabolite.

min_metabolite_sd

Minimum standard deviation required for a metabolite.

...

Additional arguments passed through the convenience wrappers.

Value

A microbe_metabolite_association object.

Examples

data("demo_crossomics", package = "microbiomedataset")

x <- calculate_correlation(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link,
  microbiome_rank = "Genus",
  metabolome_transform = "none",
  method = "spearman"
)
class(x)
#> [1] "microbe_metabolite_association"
#> attr(,"package")
#> [1] "microbiomedataset"