MeHaloCoA-package: MarinE HALOgenated COmpound Analysis

In yguitton/MeHaloCoA: Fast identification of Cl or Br containing compounds in LC-MS

Description

Fast search of compounds exhibiting chlorinated or brominated pattern (isotopic profile and mass defect) inside a hight-resolution LC-MS data set.
First Step is peakpicking with CDF2RData

Second Step is halogen Isotopic Profile search with cldetect
All Steps can be done with ONE command line runGUI
NOTE : with little modification you can search any kind of isotopic profile ([M+K]+ for example will have m2=1.998 and Thresh=7

Details

Package:	MeHaloCoA
Type:	Package
Version:	0.99.0
Date:	2014-12-09
License:	GPL (>=2)

Author(s)

Yann GUITTON, Catherine Roullier

Maintainer:Yann GUITTON <[e-mail]>

References

"Sleno, L., 2012. The use of mass defect in modern mass spectrometry: Mass defect in mass spectrometry. Journal of Mass Spectrometry 47, 226-236. doi:10.1002/jms.2953"
"Wehrens, R., Weingart, G., Mattivi, F., n.d. metaMS: An open-source pipeline for GC-MS-based untargeted metabolomics. Journal of Chromatography B. doi:10.1016/j.jchromb.2014.02.051"

Examples

runGUI()
## Not run:
## Not run: 
#Easy launch version, only ONE command line
library(MeHaloCoA)

#or
runGUI()


#command line version
library(MeHaloCoA)
#do the peak picking
data(xcmsSettings) #load peak picking parameters
an<-CDF2RData(indir = system.file("doc/mzData", package="MeHaloCoA"), settingslist=xcmsSettings)
#if indir="" interactive selection of directory

i=1 #just first file is processed with cldetect
data(cldetectSettings) #load halogens detection parameters
matcl<-do.call("cldetect", c(an[[i]],cldetectSettings))

## End(Not run)

yguitton/MeHaloCoA documentation built on May 3, 2019, 4:30 p.m.