annotate_masses: Annotate masses

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Annotate masses

Description

This function annotates masses

Usage

annotate_masses(
  features = get_params(step = "annotate_masses")$files$features$prepared,
  filter_nitro = get_params(step = "annotate_masses")$options$nitrogen_rule,
  output_annotations = get_params(step =
    "annotate_masses")$files$annotations$prepared$structural$ms1,
  output_edges = get_params(step = "annotate_masses")$files$networks$spectral$edges$raw,
  name_source = get_params(step = "annotate_masses")$names$source,
  name_target = get_params(step = "annotate_masses")$names$target,
  library = get_params(step = "annotate_masses")$files$libraries$sop$merged$keys,
  str_stereo = get_params(step =
    "annotate_masses")$files$libraries$sop$merged$structures$stereo,
  str_met = get_params(step =
    "annotate_masses")$files$libraries$sop$merged$structures$metadata,
  str_nam = get_params(step =
    "annotate_masses")$files$libraries$sop$merged$structures$names,
  str_tax_cla = get_params(step =
    "annotate_masses")$files$libraries$sop$merged$structures$taxonomies$cla,
  str_tax_npc = get_params(step =
    "annotate_masses")$files$libraries$sop$merged$structures$taxonomies$npc,
  name = get_params(step = "annotate_masses")$files$libraries$adducts$prepared,
  adducts_list = get_params(step = "annotate_masses")$ms$adducts,
  adducts_neg = get_params(step = "annotate_masses")$files$libraries$adducts$neg,
  adducts_pos = get_params(step = "annotate_masses")$files$libraries$adducts$pos,
  adducts_masses_list = system.file("extdata", "adducts.tsv", package = "timaR"),
  clusters_neg = get_params(step = "annotate_masses")$ms$clusters$neg,
  clusters_pos = get_params(step = "annotate_masses")$ms$clusters$pos,
  clusters_list = system.file("extdata", "clusters.tsv", package = "timaR"),
  neutral_losses_list = system.file("extdata", "neutral_losses.tsv", package = "timaR"),
  ms_mode = get_params(step = "annotate_masses")$ms$polarity,
  tolerance_ppm = get_params(step = "annotate_masses")$ms$tolerances$mass$ppm$ms1,
  tolerance_rt = get_params(step = "annotate_masses")$ms$tolerances$rt$minutes
)

Arguments

features	Table containing your previous annotation to complement
filter_nitro	Filter according to Nitrogen rule. Boolean
output_annotations	Output for mass based structural annotations
output_edges	Output for mass based edges
name_source	Name of the source features column
name_target	Name of the target features column
library	Library containing the keys
str_stereo	File containing structures stereo
str_met	File containing structures metadata
str_nam	File containing structures names
str_tax_cla	File containing Classyfire taxonomy
str_tax_npc	File containing NPClassifier taxonomy
name	Name of the adducts library
adducts_list	List of adducts to be used
adducts_neg	Negative adducts to be used
adducts_pos	Positive adducts to be used
adducts_masses_list	Adducts masses
clusters_neg	Negative clusters to be used
clusters_pos	Positive clusters to be used
clusters_list	List of clusters to be used
neutral_losses_list	List of neutral losses to be used
ms_mode	Ionization mode. Must be 'pos' or 'neg'
tolerance_ppm	Tolerance to perform annotation. Should be <= 10 ppm
tolerance_rt	Tolerance to group adducts. Should be <= 0.1min

Value

A table containing MS1 annotations based on exact mass

Examples

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taxonomicallyinformedannotation/tima-r documentation built on May 17, 2024, 6:30 a.m.