prepare_libraries_spectra

Prepare libraries of spectra

Description

This function prepares spectra to be used for spectral matching

Usage

prepare_libraries_spectra(
  input = get_params(step = "prepare_libraries_spectra")\$files\$libraries\$spectral\$raw,
  nam_lib = get_params(step = "prepare_libraries_spectra")\$names\$libraries,
  col_ad = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$adduct,
  col_ce = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$collision_energy,
  col_ci = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$compound_id,
  col_em = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$exact_mass,
  col_in = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$inchi,
  col_io = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$inchi_no_stereo,
  col_ik = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$inchikey,
  col_il = get_params(step =
    "prepare_libraries_spectra")\$names\$mgf\$inchikey_connectivity_layer,
  col_mf = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$molecular_formula,
  col_na = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$name,
  col_po = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$polarity,
  col_sm = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$smiles,
  col_sn = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$smiles_no_stereo,
  col_si = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$spectrum_id,
  col_sp = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$splash,
  col_sy = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$synonyms,
  col_xl = get_params(step = "prepare_libraries_spectra")\$names\$mgf\$xlogp
)

Arguments

input File containing spectra

nam_lib Metadata to identify the library

col_ad Name of the adduct in mgf

col_ce Name of the collision energy in mgf

col_ci Name of the compound id in mgf

col_em Name of the exact mass in mgf

col_in Name of the InChI in mgf

col_io Name of the InChI without stereo in mgf

col_ik Name of the InChIKey in mgf

col_il Name of the InChIKey without stereo in mgf

col_mf Name of the molecular formula in mgf

col_na Name of the name in mgf

col_po Name of the polarity in mgf

col_sm Name of the SMILES in mgf

col_sn Name of the SMILES without stereo in mgf

col_si Name of the spectrum id in mgf

col_sp Name of the SPLASH in mgf

col_sy Name of the synonyms in mgf

col_xl Name of the xlogp in mgf

polarity MS polarity

Value

The path to the prepared spectral library

Examples

library("tima")

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