RunCFMID: RunCFMID

In JustinZZW/ImmsTools: Some tools for ion mobility mass spectrometry data processing

Usage

RunCFMID(cfm_id = "F:/MetIMMS_MetFrag/cfm_id/cfm-id.exe",
  spec_file = "F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_test_result/example_spec.txt",
  id = "temp",
  candidate_file = "F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_test_result/example_candidates.txt",
  num_highest = -1, ppm_mass_tol = 10, abs_mass_tol = 0.01,
  prob_thresh = 0.001,
  param_file = "F:/MetIMMS_MetFrag/cfm_id/metab_se_cfm/param_output0.log",
  config_file = "F:/MetIMMS_MetFrag/cfm_id/metab_se_cfm/param_config.txt",
  score_type = c("Jaccard", "DotProduct"), apply_postprocessing = 1,
  output_file = "F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_output/TEST_01_result.txt",
  output_msp = "F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_output/TEST_01_spec.msp")

Arguments

cfm_id	the path of cfm_id.exe Default: 'F:/MetIMMS_MetFrag/cfm_id/cfm-id.exe'
spec_file	the path of spec_file txt file. 1st column: mz; 2nd column: intensity. It could be generated by GenerateCfmIdSpec
id	An identifier for the target molecule (Used to retrieve input spectrum from msp (if used). Default: 'temp'
num_highest	The number of (ranked) candidates to return or -1 for all. Default: -1
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). Default: 10
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). Default: 0.01
prob_thresh	The probability below which to prune unlikely fragmentations (default 0.001). Default: 0.001
param_file	This file is the output of cfm-train. Pre-trained models as used in the above publication can be found in the supplementary data for that paper stored within the source tree of this project. Here, we use the se sfm model for both positive and negative modes. Positive mode: F:/MetIMMS_MetFrag/cfm_id/metab_se_cfm/param_output0.log; Negative mode: F:/MetIMMS_MetFrag/cfm_id/negative_metab_se_cfm/param_output0.log. Default: 'F:/MetIMMS_MetFrag/cfm_id/metab_se_cfm/param_output0.log'
config_file	The filename where the configuration parameters of the cfm model can be found. This needs to match the file passed to cfm-train during training. See cfm-train documentation below for further details. Here, we use the se sfm model for both positive and negative modes. Positive mode: F:/MetIMMS_MetFrag/cfm_id/metab_se_cfm/param_config.txt; Negative mode: F:/MetIMMS_MetFrag/cfm_id/negative_metab_se_cfm/param_config.txt. Default: 'F:/MetIMMS_MetFrag/cfm_id/metab_se_cfm/param_config.txt'
score_type	The type of scoring function to use when comparing spectra. Options: Jaccard (default), DotProduct. Default: Jaccard
apply_postprocessing	Whether or not to post-process predicted spectra to take the top 80 \item output_filethe path of output result. It should be in ".txt" format. Default: 'F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_output/TEST_01_result.txt' \item output_mspthe path of output MSP file (MS/MS file). It should be in ".msp" format. Default: 'F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_output/TEST_01_spec.msp' \item spec_filethe path of spec_file txt file. 1st column: identifier; 2nd column: SMILES. It could be generated by GenerateCfmIdSpec

R interfaces to run CFM-ID.exe. Detail: https://sourceforge.net/p/cfm-id/wiki/Home/#cfm-id-precomputed RunCFMID(spec_file = 'F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_test_result/example_spec.txt', candidate_file = 'F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_test_result/example_candidates.txt', ppm_mass_tol = 10, abs_mass_tol = 0.01, score_type = 'Jaccard', output_file = 'F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_output/TEST_01_result.txt', output_msp = 'F:/MetIMMS_MetFrag/20190521_retrieve_candidates/test/cfm_id_output/TEST_01_spec.msp') Zhiwei Zhou

JustinZZW/ImmsTools documentation built on July 9, 2019, 9:32 a.m.