prepare_libraries_spectra: Prepare libraries of spectra

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

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_no_stereo,
  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

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

## End(Not run)

taxonomicallyinformedannotation/tima-r documentation built on Nov. 20, 2024, 4:34 a.m.