View source: R/weight_annotations.R
weight_annotations | R Documentation |
This function weights annotations.
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
)
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 |
score_biological_kingdom |
Score for a |
score_biological_phylum |
Score for a |
score_biological_class |
Score for a |
score_biological_order |
Score for a |
score_biological_infraorder |
Score for a |
score_biological_family |
Score for a |
score_biological_subfamily |
Score for a |
score_biological_tribe |
Score for a |
score_biological_subtribe |
Score for a |
score_biological_genus |
Score for a |
score_biological_subgenus |
Score for a |
score_biological_species |
Score for a |
score_biological_subspecies |
Score for a |
score_biological_variety |
Score for a |
score_chemical_cla_kingdom |
Score for a |
score_chemical_cla_superclass |
Score for a |
score_chemical_cla_class |
Score for a |
score_chemical_cla_parent |
Score for a |
score_chemical_npc_pathway |
Score for a |
score_chemical_npc_superclass |
Score for a |
score_chemical_npc_class |
Score for a |
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 |
annotate_masses weight_bio weight_chemo
NULL
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