Calculate Pathway Enrichment from Mechanism Links — calculate_pathway

Perform a simple over-representation analysis on pathway-linked metabolites using high-scoring mechanism links as the observed set.

Usage

calculate_pathway_enrichment(object, score_cutoff = NULL, top_n = NULL)

Arguments

object: A crossomics_mechanism object.
score_cutoff: Minimum mechanism score retained in the observed set.
top_n: Optional number of top links retained before enrichment.

Value

A data.frame of pathway enrichment statistics.

Examples

data("demo_crossomics", package = "microbiomedataset")
association <- calculate_correlation(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link,
  microbiome_rank = "Genus",
  metabolome_transform = "none"
)
pathway_link <- standardize_pathway_link(
  data.frame(
    taxon_id = summarise_taxa(
      demo_crossomics$microbiome_data,
      taxonomic_rank = "Genus"
    )@variable_info$variable_id[1],
    metabolite_id = demo_crossomics$metabolome_data@annotation_table$variable_id[1],
    pathway_id = "pathway_a",
    pathway_name = "Pathway A",
    stringsAsFactors = FALSE
  )
)
mechanism <- infer_metabolic_link(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link,
  pathway_link = pathway_link,
  association_result = association,
  microbiome_rank = "Genus",
  q_value_cutoff = 1
)
calculate_pathway_enrichment(mechanism)
#> # A tibble: 1 × 7
#>   pathway_id pathway_name n_background n_observed p_value q_value
#>   <chr>      <chr>               <int>      <int>   <dbl>   <dbl>
#> 1 pathway_a  Pathway A               1          1       1       1
#> # ℹ 1 more variable: enrichment_ratio <dbl>