weight_bio: Weight bio

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Weight bio

Description

This function weights the eventually MS1 complemented annotations according their biological source

Usage

weight_bio(
  annotation_table_taxed = get("annotation_table_taxed", envir = parent.frame()),
  structure_organism_pairs_table = get("structure_organism_pairs_table", envir =
    parent.frame()),
  weight_spectral = get("weight_spectral", envir = parent.frame()),
  weight_biological = get("weight_biological", envir = parent.frame()),
  score_biological_domain = get("score_biological_domain", envir = parent.frame()),
  score_biological_kingdom = get("score_biological_kingdom", envir = parent.frame()),
  score_biological_phylum = get("score_biological_phylum", envir = parent.frame()),
  score_biological_class = get("score_biological_class", envir = parent.frame()),
  score_biological_order = get("score_biological_order", envir = parent.frame()),
  score_biological_family = get("score_biological_family", envir = parent.frame()),
  score_biological_tribe = get("score_biological_tribe", envir = parent.frame()),
  score_biological_genus = get("score_biological_genus", envir = parent.frame()),
  score_biological_species = get("score_biological_species", envir = parent.frame()),
  score_biological_variety = get("score_biological_variety", envir = parent.frame())
)

Arguments

annotation_table_taxed	Table containing the initial annotation eventually complemented by additional MS1 annotations
structure_organism_pairs_table	Table containing the structure - organism pairs
weight_spectral	Weight for the spectral score
weight_biological	Weight for the biological score
score_biological_domain	Score for a domain match (should be lower than kingdom)
score_biological_kingdom	Score for a kingdom match (should be lower than phylum)
score_biological_phylum	Score for a phylum match (should be lower than class)
score_biological_class	Score for a class match (should be lower than order)
score_biological_order	Score for a order match (should be lower than family)
score_biological_family	Score for a family match (should be lower than tribe)
score_biological_tribe	Score for a tribe match (should be lower than genus)
score_biological_genus	Score for a genus match (should be lower than species)
score_biological_species	Score for a species match (should be lower than variety)
score_biological_variety	Score for a variety match (should be the highest)

Value

A table containing the biologically weighted annotation

Examples

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taxonomicallyinformedannotation/tima-r documentation built on Nov. 20, 2024, 4:34 a.m.