Prepare annotations GNPS

Description

This function prepares GNPS spectral library matching results by standardizing column names, integrating structure metadata, and formatting for downstream TIMA annotation workflows.

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	character Character string or vector of paths to GNPS annotation files
output	character Character string path for prepared GNPS annotations output
str_stereo	character Character string path to structures stereochemistry file
str_met	character Character string path to structures metadata file
str_nam	character Character string path to structures names file
str_tax_cla	character Character string path to ClassyFire taxonomy file
str_tax_npc	character Character string path to NPClassifier taxonomy file

Value

Character string path to prepared GNPS annotations

See Also

Other preparation: prepare_annotations_mzmine(), prepare_annotations_sirius(), prepare_annotations_spectra(), prepare_features_components(), prepare_features_edges(), prepare_features_tables(), prepare_libraries_rt(), prepare_libraries_sop_bigg(), prepare_libraries_sop_closed(), prepare_libraries_sop_ecmdb(), prepare_libraries_sop_hmdb(), prepare_libraries_sop_lotus(), prepare_libraries_sop_merged(), prepare_libraries_spectra(), prepare_params(), prepare_taxa()

Examples

library("tima")

copy_backbone()
go_to_cache()
prepare_annotations_gnps()
unlink("data", recursive = TRUE)