weight_chemo: Weight chemo

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Weight chemo

Description

This function weights the biologically weighted annotations according their chemical consistency

Usage

weight_chemo(
  annot_table_wei_bio_clean = get("annot_table_wei_bio_clean", envir = parent.frame()),
  weight_spectral = get("weight_spectral", envir = parent.frame()),
  weight_biological = get("weight_biological", envir = parent.frame()),
  weight_chemical = get("weight_chemical", envir = parent.frame()),
  score_chemical_cla_kingdom = get("score_chemical_cla_kingdom", envir = parent.frame()),
  score_chemical_cla_superclass = get("score_chemical_cla_superclass", envir =
    parent.frame()),
  score_chemical_cla_class = get("score_chemical_cla_class", envir = parent.frame()),
  score_chemical_cla_parent = get("score_chemical_cla_parent", envir = parent.frame()),
  score_chemical_npc_pathway = get("score_chemical_npc_pathway", envir = parent.frame()),
  score_chemical_npc_superclass = get("score_chemical_npc_superclass", envir =
    parent.frame()),
  score_chemical_npc_class = get("score_chemical_npc_class", envir = parent.frame())
)

Arguments

annot_table_wei_bio_clean	Table containing the biologically weighted annotation
weight_spectral	Weight for the spectral score
weight_biological	Weight for the biological score
weight_chemical	Weight for the chemical consistency score
score_chemical_cla_kingdom	Score for a ⁠Classyfire kingdom⁠ match (should be lower than ⁠ Classyfire superclass⁠)
score_chemical_cla_superclass	Score for a ⁠Classyfire superclass⁠ match (should be lower than ⁠Classyfire class⁠)
score_chemical_cla_class	Score for a ⁠Classyfire class⁠ match (should be lower than ⁠Classyfire parent⁠)
score_chemical_cla_parent	Score for a ⁠Classyfire parent⁠ match (should be the highest)
score_chemical_npc_pathway	Score for a pathway match (should be lower than superclass)
score_chemical_npc_superclass	Score for a superclass match (should be lower than class)
score_chemical_npc_class	Score for a class match (should be the highest)

Value

A table containing the chemically weighted annotation

Examples

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taxonomicallyinformedannotation/tima-r documentation built on Dec. 20, 2024, 9:32 a.m.