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Standardize Pathway Link Metadata

Source: R/utils_microbiome.R
standardize_pathway_link.Rd

Normalize a cross-omics pathway link table to the schema used by infer_metabolic_link().

Usage

standardize_pathway_link(pathway_link)

Arguments

A pathway link table.

Value

A standardized pathway link table.

Examples

pathway_link <- data.frame(
  taxon_id = "Genus_A",
  metabolite_id = "M1",
  pathway_id = "pathway_1"
)
standardize_pathway_link(pathway_link)
#>   taxon_id metabolite_id pathway_id pathway_name reaction_id reaction_name
#> 1  Genus_A            M1  pathway_1         <NA>        <NA>          <NA>
#>   evidence_type compound_name annotation_level
#> 1 user_supplied          <NA>             <NA>