cfm_id_precomputed: CFM-ID Precomupted

In gjgetzinger/cfmR: R Wrapper for calling the Competitive Fragmentation Modeling for Metabolite Identifiction (CFM-ID) algorithm

Description

CFM-ID Precomupted

Usage

cfm_id_precomputed(
  spectrum_file,
  id,
  candidate_file,
  num_highest,
  ppm_mass_tol,
  abs_mass_tol,
  score_type,
  output_filename
)

Arguments

spectrum_file	The filename where the input spectra can be found. This can be a .msp file in which the desired spectrum is listed under a corresponding id (next arg). Or it could be a single file with a list of peaks 'mass intensity' delimited by lines, with either 'low','med' and 'high' lines beginning spectra of different energy levels, or 'energy0', 'energy1', etc.
id	An identifier for the target molecule (printed to output, in case of multiple concatenated results, and used to retrieve input spectrum from msp where msp is used).
candidate_file	The filename where the input list of candidate structures can be found - line separated 'id smiles_or_inchi spectrum_file' triples, where the spectrum file stores the precomputed spectra (no spaces allowed).
num_highest	The number of (ranked) candidates to return or -1 for all (if not given, returns all in ranked order)
ppm_mass_tol	The mass tolerance in ppm to use when matching peaks within the dot product comparison - will use higher resulting tolerance of ppm and abs (if not given defaults to 10ppm)
abs_mass_tol	The mass tolerance in abs Da to use when matching peaks within the dot product comparison - will use higher resulting tolerance of ppm and abs ( if not given defaults to 0.01Da)
score_type	The type of scoring function to use when comparing spectra. Options: Jaccard (default), DotProduct
output_filename	The filename of the output file to write to (if not given, prints to stdout)

gjgetzinger/cfmR documentation built on May 11, 2020, 1 p.m.