MISA R package

This package is the source code of the MISA algorithm, a strategy to annotate in-source fragments from the METLIN database.

This repository containts the source code, and a small sample MySQL database, only for developers. Users are encouraged to use the online version of MISA available at http://xcmsonline.scripps.edu

If you use the package MISA in your analysis and publications please cite:

Domingo-Almenara, X., Montenegro-Burke, J. R., Guijas, C., Majumder, E. L-W., Benton, H. P., Siuzdak, G. Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics. Analytical Chemistry 91 (2019) 3246–3253. DOI: 10.1021/acs.analchem.8b03126

Getting Started

Prerequisites

You need to have a MySQL installed in your computer. You can use the sample MySQL DB distributed with misaR, and install it in your computer.

Installing

You need to compile (requieres compilation using Rcpp) and install misaR.

R CMB build misaR
R CMD install  misaR_0.1.0.tar.gz 

Running the tests

You can use a diffreport from XCMSOnline with misaR, an execute it via:

Load package and define parameters

library(misaR)

## SOFTWARE PARAMETERS:
gpar <- new("inSApar", ppm.error = 20, clust.rt = 2, mz.error = 0.01, ion.mode='+', block.size=10)
dbCred <- list(user='dbuser', password='test12', dbname='misa_db', host='localhost')
fileName <- 'testReport.tsv'
isRTinMinutes <- 'Y'

Read diffreport and convert minutes to seconds if necessary

annTab <- read.delim(fileName)
if(isRTinMinutes=='Y') annTab[,'rtmed'] <- annTab[,'rtmed']*60

Execute MISA:

annTabu <- inSourceAnnotation(annTab=annTab, dbCred=dbCred, gpar=gpar)

Authors

• Xavier Domingo-Almenara - Initial work

License

This project is licensed under the MIT License - see the LICENCE file for details