Weight annotations

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$compounds_names,
  high_confidence = get_params(step = "weight_annotations")$options$high_confidence,
  remove_ties = get_params(step = "weight_annotations")$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
high_confidence: Report high confidence candidates only. 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

Value

The path to the weighted annotations

Examples

if (FALSE) { # \dontrun{
tima:::copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
library <- get_params(step = "weight_annotations")$files$libraries$sop$merged$keys |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
org_tax_ott <- get_params(step = "weight_annotations")$files$libraries$sop$merged$organisms$taxonomies$ott |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
str_stereo <- get_params(step = "weight_annotations")$files$libraries$sop$merged$structures$stereo |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
annotations <- get_params(step = "weight_annotations")$files$annotations$filtered |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
canopus <- get_params(step = "weight_annotations")$files$annotations$prepared$canopus |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
formula <- get_params(step = "weight_annotations")$files$annotations$prepared$formula |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
components <- get_params(step = "weight_annotations")$files$networks$spectral$components$prepared |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
edges <- get_params(step = "weight_annotations")$files$networks$spectral$edges$prepared |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
taxa <- get_params(step = "weight_annotations")$files$metadata$prepared |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
get_file(url = paste0(dir, library), export = library)
get_file(url = paste0(dir, org_tax_ott), export = org_tax_ott)
get_file(url = paste0(dir, str_stereo), export = str_stereo)
get_file(url = paste0(dir, annotations), export = annotations)
get_file(url = paste0(dir, canopus), export = canopus)
get_file(url = paste0(dir, formula), export = formula)
get_file(url = paste0(dir, components), export = components)
get_file(url = paste0(dir, edges), export = edges)
get_file(url = paste0(dir, taxa), export = taxa)
weight_annotations(
  library = library,
  org_tax_ott = org_tax_ott,
  str_stereo = str_stereo,
  annotations = annotations,
  canopus = canopus,
  formula = formula,
  components = components,
  edges = edges,
  taxa = taxa
)
unlink("data", recursive = TRUE)
} # }

Usage

Arguments

Value

See also

Examples