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Weight annotations

Source: R/weight_annotations.R
weight_annotations.Rd

This function weights annotations.

Usage

weight_annotations(
  library = get_params(step = "weight_annotations")$files$libraries$sop$merged$keys,
  org_tax_ott = get_params(step =
    "weight_annotations")$files$libraries$sop$merged$organisms$taxonomies$ott,
  str_stereo = get_params(step =
    "weight_annotations")$files$libraries$sop$merged$structures$stereo,
  annotations = get_params(step = "weight_annotations")$files$annotations$filtered,
  canopus = get_params(step = "weight_annotations")$files$annotations$prepared$canopus,
  formula = get_params(step = "weight_annotations")$files$annotations$prepared$formula,
  components = get_params(step =
    "weight_annotations")$files$networks$spectral$components$prepared,
  edges = get_params(step = "weight_annotations")$files$networks$spectral$edges$prepared,
  taxa = get_params(step = "weight_annotations")$files$metadata$prepared,
  output = get_params(step = "weight_annotations")$files$annotations$processed,
  candidates_final = get_params(step = "weight_annotations")$annotations$candidates$final,
  weight_spectral = get_params(step = "weight_annotations")$weights$global$spectral,
  weight_chemical = get_params(step = "weight_annotations")$weights$global$chemical,
  weight_biological = get_params(step = "weight_annotations")$weights$global$biological,
  score_biological_domain = get_params(step =
    "weight_annotations")$weights$biological$domain,
  score_biological_kingdom = get_params(step =
    "weight_annotations")$weights$biological$kingdom,
  score_biological_phylum = get_params(step =
    "weight_annotations")$weights$biological$phylum,
  score_biological_class = get_params(step =
    "weight_annotations")$weights$biological$class,
  score_biological_order = get_params(step =
    "weight_annotations")$weights$biological$order,
  score_biological_infraorder = get_params(step =
    "weight_annotations")$weights$biological$infraorder,
  score_biological_family = get_params(step =
    "weight_annotations")$weights$biological$family,
  score_biological_subfamily = get_params(step =
    "weight_annotations")$weights$biological$subfamily,
  score_biological_tribe = get_params(step =
    "weight_annotations")$weights$biological$tribe,
  score_biological_subtribe = get_params(step =
    "weight_annotations")$weights$biological$subtribe,
  score_biological_genus = get_params(step =
    "weight_annotations")$weights$biological$genus,
  score_biological_subgenus = get_params(step =
    "weight_annotations")$weights$biological$subgenus,
  score_biological_species = get_params(step =
    "weight_annotations")$weights$biological$species,
  score_biological_subspecies = get_params(step =
    "weight_annotations")$weights$biological$subspecies,
  score_biological_variety = get_params(step =
    "weight_annotations")$weights$biological$variety,
  score_chemical_cla_kingdom = get_params(step =
    "weight_annotations")$weights$chemical$cla$kingdom,
  score_chemical_cla_superclass = get_params(step =
    "weight_annotations")$weights$chemical$cla$superclass,
  score_chemical_cla_class = get_params(step =
    "weight_annotations")$weights$chemical$cla$class,
  score_chemical_cla_parent = get_params(step =
    "weight_annotations")$weights$chemical$cla$parent,
  score_chemical_npc_pathway = get_params(step =
    "weight_annotations")$weights$chemical$npc$pathway,
  score_chemical_npc_superclass = get_params(step =
    "weight_annotations")$weights$chemical$npc$superclass,
  score_chemical_npc_class = get_params(step =
    "weight_annotations")$weights$chemical$npc$class,
  minimal_consistency = get_params(step =
    "weight_annotations")$annotations$thresholds$consistency,
  minimal_ms1_bio = get_params(step =
    "weight_annotations")$annotations$thresholds$ms1$biological,
  minimal_ms1_chemo = get_params(step =
    "weight_annotations")$annotations$thresholds$ms1$chemical,
  minimal_ms1_condition = get_params(step =
    "weight_annotations")$annotations$thresholds$ms1$condition,
  ms1_only = get_params(step = "weight_annotations")$annotations$ms1only,
  compounds_names = get_params(step = "weight_annotations")$options$compounds_names,
  remove_ties = get_params(step = "weight_annotations")$options$remove_ties,
  summarise = get_params(step = "weight_annotations")$options$summarise,
  pattern = get_params(step = "weight_annotations")$files$pattern,
  force = get_params(step = "weight_annotations")$options$force
)

Arguments

library

Library containing the keys

org_tax_ott

File containing organisms taxonomy (OTT)

str_stereo

File containing structures stereo

annotations

Prepared annotations file

canopus

Prepared canopus file

formula

Prepared formula file

components

Prepared components file

edges

Prepared edges file

taxa

Prepared taxed features file

output

Output file

candidates_final

Number of final candidates to keep

weight_spectral

Weight for the spectral score

weight_chemical

Weight for the biological score

weight_biological

Weight for the chemical consistency 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 infraorder)

score_biological_infraorder

Score for a infraorder match (should be lower than order)

score_biological_family

Score for a family match (should be lower than subfamily)

score_biological_subfamily

Score for a subfamily match (should be lower than family)

score_biological_tribe

Score for a tribe match (should be lower than subtribe)

score_biological_subtribe

Score for a subtribe match (should be lower than genus)

score_biological_genus

Score for a genus match (should be lower than subgenus)

score_biological_subgenus

Score for a subgenus match (should be lower than species)

score_biological_species

Score for a species match (should be lower than subspecies)

score_biological_subspecies

Score for a subspecies match (should be lower than variety)

score_biological_variety

Score for a variety match (should be the highest)

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 NPC pathway match (should be lower than NPC superclass)

score_chemical_npc_superclass

Score for a NPC superclass match (should be lower than NPC class)

score_chemical_npc_class

Score for a NPC class match (should be the highest)

minimal_consistency

Minimal consistency score for a class. FLOAT

minimal_ms1_bio

Minimal biological score to keep MS1 based annotation

minimal_ms1_chemo

Minimal chemical score to keep MS1 based annotation

minimal_ms1_condition

Condition to be used. Must be "OR" or "AND".

ms1_only

Keep only MS1 annotations. BOOLEAN

compounds_names

Report compounds names. Can be very large. BOOLEAN

remove_ties

Remove ties. BOOLEAN

summarise

Summarize results (1 row per feature). BOOLEAN

pattern

Pattern to identify your job. STRING

force

Force parameters. Use it at your own risk

See also

annotate_masses weight_bio weight_chemo

Examples

NULL
#> NULL