import.sirius: import.sirius

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

import.sirius

Description

After running Sirius on .ms files, import the annotation results

Usage

import.sirius(ramclustObj = NULL, ms.dir = NULL, ion.mode = NULL)

Arguments

ramclustObj	R object - the ramclustR object which was used to write the .mat or .msp files
ms.dir	optional path to .mat directory. default = "spectra/ms/out" subdirectory in working directory
ion.mode	specify either "N" for negative ionization mode or "P" for positive ionization mode

Details

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

Value

an updated ramclustR object, with new slots at $msfinder.sirius

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.

cbroeckl/csu.pmf.tools documentation built on Jan. 26, 2024, 6:27 p.m.