xcmsSettings: Example settings for MeHaloCoA peakpicking

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

Description

example settings needed for function CDF2RData, theses settings are mainly parameters for peakpicking with xcms and CAMERA. for CAMERA only groupFWHM is used. you can add mzrange for ex mzrange=c(100,1000) or/and rtrange (in minutes) rtrange=c(5,15)

Usage

data(xcmsSettings)

Format

The format is a list with any xcmsSet parameters and if wanted you can add perfwhm parameter from groupFWHM value. e.g mySettings<-list(fwhm=15,snthresh=3,step=0.01,mzdiff=0.05, perfwhm=0.6)

Details

The base of the settings are taken from metaMS package see references

Source

"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

data(xcmsSettings)
#see all parameters
xcmsSettings

#if you want to change a parameter
xcmsSettings$perfwhm<-0.80

#if you want to add a new parameter
xcmsSettings$nSlaves<-1

#if you want to remove a parameter
xcmsSettings$nSlaves<-NULL


#if you want to create a complete list of parameters
myparam<-list(perfwhm=0.6,
				snthresh=3,
				max=50,
				step=0.01,
				steps=2,
				mzdiff=0.05,
				profmethod="bin",
				nSlaves=1)

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