import.msfinder.formulas: import.MSFinder.formulas

Description Usage Arguments Details Value Author(s) References

View source: R/import.MSFinder.formulas.R

Description

After running MSFinder on .mat or .msp files, import the formulas that were predicted and their scores

Usage

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import.msfinder.formulas(ramclustObj = RC, mat.dir = NULL, msp.dir = NULL,
  database.priority = NULL)

Arguments

ramclustObj

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

mat.dir

optional path to .mat directory

database.priority

character. Can be set to a single or multiple database names. must match database names as they are listed in MSFinder precisily. Can also be set to 'all' (note that MSFinder reports all databases matched, not just selected databases). If any database is set, the best formula match to that (those) database(s) is selected, rather than the best formula match overall.

msp.dor

optional path to .msp directory

Details

this function imports the output from the MSFinder program to annotate the ramclustR object

Value

new slots at $msfinder.formula, $msfinder.formula.score, and $msfinder.formula.details

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 June 22, 2018, 4:22 p.m.