weight_annotations: Weight annotations

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Weight annotations

Description

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

See Also

annotate_masses weight_bio weight_chemo

Examples

## Not run: 
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)

## End(Not run)

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