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Prepare libraries of spectra

Source: R/prepare_libraries_spectra.R
prepare_libraries_spectra.Rd

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

if (FALSE) { # \dontrun{
tima:::copy_backbone()
go_to_cache()
prepare_libraries_spectra()
unlink("data", recursive = TRUE)
} # }