prepare_annotations_sirius: Prepare annotations SIRIUS

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Prepare annotations SIRIUS

Description

This function prepares Sirius results to make them compatible

Usage

prepare_annotations_sirius(
  input_directory = get_params(step =
    "prepare_annotations_sirius")$files$annotations$raw$sirius,
  output_ann = get_params(step =
    "prepare_annotations_sirius")$files$annotations$prepared$structural$sirius,
  output_can = get_params(step =
    "prepare_annotations_sirius")$files$annotations$prepared$canopus,
  output_for = get_params(step =
    "prepare_annotations_sirius")$files$annotations$prepared$formula,
  sirius_version = get_params(step = "prepare_annotations_sirius")$tools$sirius$version,
  str_stereo = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$stereo,
  str_met = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$metadata,
  str_nam = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$names,
  str_tax_cla = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$taxonomies$cla,
  str_tax_npc = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$taxonomies$npc
)

Arguments

input_directory	Directory containing the Sirius results
output_ann	Output where to save prepared annotation results
output_can	Output where to save prepared canopus results
output_for	Output where to save prepared formula results
sirius_version	Sirius version
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 SIRIUS annotations

Examples

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

## End(Not run)

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