library("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 <- paste0(
"data/interim/libraries/",
"sop/merged/organisms/taxonomies/ott.tsv"
)
str_stereo <- paste0(
"data/interim/libraries/",
"sop/merged/structures/stereo.tsv"
)
annotations <- paste0(
"data/interim/annotations/",
"example_annotationsFiltered.tsv"
)
canopus <- paste0(
"data/interim/annotations/",
"example_canopusPrepared.tsv"
)
formula <- paste0(
"data/interim/annotations/",
"example_formulaPrepared.tsv"
)
components <- paste0(
"data/interim/features/",
"example_componentsPrepared.tsv"
)
edges <- paste0(
"data/interim/features/",
"example_edges.tsv"
)
taxa <- paste0(
"data/interim/taxa/",
"example_taxed.tsv"
)
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)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_neighbors = get_params(step =
"weight_annotations")\$annotations\$candidates\$neighbors,
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,
summarize = get_params(step = "weight_annotations")\$options\$summarize,
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_neighbors
|
Number of neighbors candidates to keep |
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 |
summarize
|
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