get_gnps_tables: Get GNPS Tables

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Get GNPS Tables

Description

This function gets GNPS tables from corresponding job ID.

Usage

get_gnps_tables(
  gnps_job_id,
  gnps_job_example = get_default_paths()$gnps$example,
  filename,
  workflow = "fbmn",
  path_features,
  path_metadata,
  path_spectra,
  path_source = get_default_paths()$data$source$path,
  path_interim_a = get_default_paths()$data$interim$annotations$path,
  path_interim_f = get_default_paths()$data$interim$features$path
)

Arguments

gnps_job_id	GNPS job ID
gnps_job_example	GNPS job example
filename	Name of the file
workflow	Character string indicating the type of workflow, either "fbmn" or "classical"
path_features	Path to features
path_metadata	Path to metadata
path_spectra	Path to spectra
path_source	Path to store the source files
path_interim_a	Path to store the interim annotations file
path_interim_f	Path to store the interim features files

Value

The downloaded GNPS tables

Examples

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