Associate Microbiome Taxa with Metabolites — associate_microbe

Compute pairwise microbe-metabolite associations on matched samples.

Usage

associate_microbe_metabolite(
  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"
)

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.

Value

A microbe_metabolite_association object.

Examples

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

x <- create_microbiome_metabolome_dataset(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link
)
y <- associate_microbe_metabolite(x, microbiome_rank = "Genus")
#> Warning: NaNs produced
class(y)
#> [1] "microbe_metabolite_association"
#> attr(,"package")
#> [1] "microbiomedataset"