Prepare annotations MS2

Description

This function prepares the spectral matches obtained previously to make them compatible

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	Input file
output	Output file
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

Value

The path to the 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)