annotate_masses: Annotate masses

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Annotate masses

Description

This function annotates a feature table based on exact mass match. It requires a structural library, its metadata, and lists of adducts, clusters, and neutral losses to be considered. The polarity has to be pos or neg and retention time and mass tolerances should be given. The feature table is expected to be pre-formatted.

Usage

annotate_masses(
  features = get_params(step = "annotate_masses")$files$features$prepared,
  output_annotations = get_params(step =
    "annotate_masses")$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,
  adducts_list = get_params(step = "annotate_masses")$ms$adducts,
  clusters_list = get_params(step = "annotate_masses")$ms$clusters,
  neutral_losses_list = get_params(step = "annotate_masses")$ms$neutral_losses,
  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$adducts
)

Arguments

features	Table containing your previous annotation to complement
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
adducts_list	List of adducts 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 <= 20 ppm
tolerance_rt	Tolerance to group adducts. Should be <= 0.05 minutes

Value

The path to the files containing MS1 annotations and edges

Examples

## Not run: 
tima:::copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
data_interim <- "data/interim/"
dir <- paste0(github, repo)
dir <- paste0(dir, data_interim)
annotate_masses(
  features = paste0(dir, "features/example_features.tsv"),
  library = paste0(dir, "libraries/sop/merged/keys.tsv"),
  str_stereo = paste0(dir, "libraries/sop/merged/structures/stereo.tsv"),
  str_met = paste0(dir, "libraries/sop/merged/structures/metadata.tsv"),
  str_nam = paste0(dir, "libraries/sop/merged/structures/names.tsv"),
  str_tax_cla = paste0(dir, "libraries/sop/merged/structures/taxonomies/classyfire.tsv"),
  str_tax_npc = paste0(dir, "libraries/sop/merged/structures/taxonomies/npc.tsv")
)
unlink("data", recursive = TRUE)

## End(Not run)

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