cfm_predict: CFM-predict

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

Description

CFM-predict

Usage

cfm_predict(
  input_smiles_or_inchi,
  prob_thresh_for_prune = 0.001,
  param_filename,
  config_filename,
  include_annotations = 0,
  output_filename = NULL,
  apply_post_processing = 1
)

Arguments

input_smiles_or_inchi	The smiles or inchi string of the structure whose spectra you want to predict.
prob_thresh_for_prune	The probability below which to prune unlikely fragmentations (default 0.001)
param_filename	The filename where the parameters of a trained cfm model can be found (if not given, assumes param_output.log in current directory)
config_filename	The filename where the configuration parameters of the cfm model can be found (if not given, assumes param_config.txt in current directory)
include_annotations	Whether to include fragment information in the output spectra (0 = NO (default), 1 = YES ). Note: ignored for msp/mgf output.
output_filename	The filename of the output spectra file to write to (if not given, returns list from stdout).
apply_post_processing	Whether or not to post-process predicted spectra to take the top 80 (whichever comes first) (0 = OFF, 1 = ON (default) ).

Value

When a output filename is provided, the path to the file. If no filename is provided, results are extracted from the standard output into a named list.

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