export.msfinder.formulas: export MSFinder formula prediction results in tabular format.

View source: R/export.msfinder.formulas.R

export.msfinder.formulasR Documentation

export MSFinder formula prediction results in tabular format.

Description

After running MSFinder, results have been imported to the ramclustR object. This function exports as a .csv file for ease of viewing.

Usage

export.msfinder.formulas(
  ramclustObj = NULL,
  export.all = FALSE,
  output.directory = NULL
)

Arguments

ramclustObj

R object - the ramclustR object which was used to write the .mat or .msp files

export.all

logical: default = FALSE. If TRUE, export all columns, if FALSE, only columns 1: "exactmass"

output.directory

valid path: default = NULL. If NULL, results are exported to spectra/mat directory.

Details

this function exports a .csv file containing all returned MSFinder molecular formula hypotheses. this file is saved (by default) to the working directory spectra/mat/ directory

Value

an updated ramclustR object, with the RC$ann and RC$ann.conf slots updated to annotated based on output from 1. ramsearch output, 2. msfinder mssearch, 3. msfinder predicted structure, 4. msfinder predicted formula, and 5. interpretMSSpectrum inferred molecular weight, with listed order as priority.

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.


cbroeckl/csu.pmf.tools documentation built on May 21, 2024, 1:26 a.m.