prepare_annotations_gnps: Prepare annotations GNPS

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Prepare annotations GNPS

Description

This function prepares GNPS obtained annotations

Usage

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

Examples

## Not run: 
tima:::copy_backbone()
go_to_cache()
prepare_annotations_gnps()
unlink("data", recursive = TRUE)

## End(Not run)

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