Skip to contents

Weight bio

Source: R/weight_bio.R
weight_bio.Rd

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

NULL
#> NULL