Summarize Reaction-Level Mechanisms — summarise

Aggregate mechanism evidence from taxon-metabolite links to reaction-level summaries, optionally incorporating taxon-to-reaction mappings.

Usage

summarise_reactions(mechanism_result, taxon_reaction_link = NULL)

Arguments

mechanism_result: A crossomics_mechanism object.
taxon_reaction_link: Optional taxon-to-reaction link table.

Value

A reaction summary data.frame.

Examples

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

pathway_link <- standardize_pathway_link(
  data.frame(
    taxon_id = summarise_taxa(
      demo_crossomics$microbiome_data,
      taxonomic_rank = "Genus"
    )@variable_info$variable_id[1],
    metabolite_id = demo_crossomics$metabolome_data@annotation_table$variable_id[1],
    pathway_id = "pathway_a",
    reaction_id = "reaction_a",
    reaction_name = "Reaction A",
    stringsAsFactors = FALSE
  )
)
mechanism <- infer_metabolic_link(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link,
  pathway_link = pathway_link,
  microbiome_rank = "Genus",
  q_value_cutoff = 1
)
#> Warning: NaNs produced
summarise_reactions(mechanism)
#> # A tibble: 1 × 8
#>   reaction_id reaction_name pathway_id pathway_name n_taxa n_metabolites
#>   <chr>       <chr>         <chr>      <chr>         <int>         <int>
#> 1 reaction_a  Reaction A    pathway_a  NA                1             1
#> # ℹ 2 more variables: mean_mechanism_score <dbl>, max_mechanism_score <dbl>