do.msfinder: do.msfinder

In sneumann/RAMClustR: RAMClust: a novel feature clustering method enables spectral-matching based annotation for metabolomics data

Description

Call MSFinder from R. Currently requires clunky pasting into cmd prompt.

Usage

  do.msfinder(msfinder.dir = "K:/software/MSFinder/MS-FINDER program ver. 2.20",
  which.function = "predict", mat.dir = NULL, msp.dir = NULL)

Arguments

msfinder.dir	full path to the directory containing the MSFinderConsoleApp exe file
which.function	character - one of "predict" or "mssearch" - see MSFinder console application description for details
mat.dir	by default, ramclustR will look in the working directory for a spectra/mat or spectra/msp subdirectory. Else specify the path here for mat formatted spectra (all spectra in directory will be used)
msp.idr	by default, ramclustR will look in the working directory for a spectra/mat or spectra/msp subdirectory. Else specify the path here for msp formatted spectra (all spectra in directory will be used)

Details

calls the 'MsfinderConsoleApp.exe' 'predict' program. Ensure before calling that you have set appropriate parameters in the 'MSFINDER.INI' file

Value

nothing is returned. All output is saved by MSFinder in the relevent mat or msp directory. Data can be imported using the import.msfinder.formulas() and import.msfinder.structure() commands after processing has finished

Author(s)

Corey Broeckling

References

Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014 Jul 15;86(14):6812-7. doi: 10.1021/ac501530d. Epub 2014 Jun 26. PubMed PMID: 24927477.

Broeckling CD, Ganna A, Layer M, Brown K, Sutton B, Ingelsson E, Peers G, Prenni JE. Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction. Anal Chem. 2016 Sep 20;88(18):9226-34. doi: 10.1021/acs.analchem.6b02479. Epub 2016 Sep 8. PubMed PMID: 7560453.

Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, Cajka T, Saito K, Fiehn O, Arita M. Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. Anal Chem. 2016 Aug 16;88(16):7946-58. doi: 10.1021/acs.analchem.6b00770. Epub 2016 Aug 4. PubMed PMID: 27419259.

sneumann/RAMClustR documentation built on May 30, 2019, 5:05 a.m.