Infer Mechanistic Microbe-Metabolite Links — infer_metabolic

Combine statistical association results with a pathway link table and standardized metabolite annotation to create a mechanism-oriented evidence table.

Usage

infer_metabolic_link(
  object = NULL,
  microbiome_data = NULL,
  metabolome_data = NULL,
  sample_link = NULL,
  pathway_link = NULL,
  association_result = NULL,
  microbiome_rank = "Genus",
  q_value_cutoff = 0.1
)

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.
pathway_link: Optional pathway link table used when object is not supplied.
association_result: Optional microbe_metabolite_association result. If missing, associations are computed internally.
microbiome_rank: Taxonomy rank for microbiome aggregation.
q_value_cutoff: Significance threshold used to keep statistical links.

Value

A crossomics_mechanism object.

Examples

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

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

pathway_link <- data.frame(
  taxon_id = demo_crossomics$microbiome_data@variable_info$Genus[1],
  metabolite_id = demo_crossomics$metabolome_data@variable_info$variable_id[1],
  pathway_id = "pathway_1",
  evidence_type = "annotation_overlap"
)

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