Prepare annotations MS2

Description

This function prepares MS2 spectral library matching results by standardizing column names, integrating structure metadata, and formatting for downstream TIMA annotation workflows. Handles various spectral matching result formats.

Usage

prepare_annotations_spectra(
  input = get_params(step =
    "prepare_annotations_spectra")\$files\$annotations\$raw\$spectral\$spectral,
  output = get_params(step =
    "prepare_annotations_spectra")\$files\$annotations\$prepared\$structural\$spectral,
  str_stereo = get_params(step =
    "prepare_annotations_spectra")\$files\$libraries\$sop\$merged\$structures\$stereo,
  str_met = get_params(step =
    "prepare_annotations_spectra")\$files\$libraries\$sop\$merged\$structures\$metadata,
  str_nam = get_params(step =
    "prepare_annotations_spectra")\$files\$libraries\$sop\$merged\$structures\$names,
  str_tax_cla = get_params(step =
    "prepare_annotations_spectra")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
  str_tax_npc = get_params(step =
    "prepare_annotations_spectra")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc
)

Arguments

input	Character string path to spectral matching results file
output	Character string path for prepared spectral annotations output
str_stereo	Character string path to structures stereochemistry file
str_met	Character string path to structures metadata file
str_nam	Character string path to structures names file
str_tax_cla	Character string path to ClassyFire taxonomy file
str_tax_npc	Character string path to NPClassifier taxonomy file

Value

Character string path to prepared spectral annotations

Examples

library("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)
input <- get_params(step = "prepare_annotations_spectra")$files$annotations$raw$spectral$spectral |>
  gsub(pattern = ".tsv.gz", replacement = "_pos.tsv", fixed = TRUE)
get_file(url = paste0(dir, input), export = input)
dir <- paste0(dir, data_interim)
prepare_annotations_spectra(
  input = input,
  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)