CDF2RData: CDF2RData is a function to do peakpicking based on _xcms and...

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

Description

CDF2RData is a function to do peakpicking based on xcms and CAMERA, the base of the code is from R. Wehrens and was addapted for the MeHaloCoA package

Usage

CDF2RData(indir = "", outdir=NULL, files=NULL, settingslist)

Arguments

indir	The directory where your converted LC-MS data are (accepted format are mzML, mzXML, mzData, CDF) see mzR package for more details on formats if indir="" (default) the selection of your data repository is interactive
outdir	The directory where the results have to be saved, if NULL (default) your working directory is used
files	Default= NULL, if you don't want to process all the files in indir you can use the files parameter. The path to the file(s) you want to be processed (accepted format are mzML, mzXML, mzData, CDF) see mzR package for more details on formats. e.g : files=c("c:/mydocs/file1.mzML", "c:/mydocs/files32.mzML")
settingslist	settingslist a peakpicking setting list as xcmsSettings. ex: mylist<-list(method="matchedFilter",ppm=15,mzdiff=0.05,rtrange=c(5,15), mzrange=c(100,500))

Value

A list of xsAnnotate objects with each slot being the result of xcms and CAMERA peakpicking process, a slot named samples is added to that list with sample names, and an other names settings keep track of your peakpicking parameters two files are saved in outdir: an.rda with xsAnnotate list and settings.rda with your settings

Note

Many Thanks to R. Wherens for the starting codes

Author(s)

Yann GUITTON

References

"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"

See Also

xcmsSettings

Examples

runGUI()
## Not run: 
## Not run:
data(xcmsSettings)
an<-CDF2RData(indir = system.file("doc/mzData", package="MeHaloCoA"), settingslist=xcmsSettings)

## or with files option
data(xcmsSettings)
myfile<-file.path(system.file("doc/mzData", package="MeHaloCoA"),"Q-ToF_Data1.mzData")
an<-CDF2RData(files=myfile, settingslist=xcmsSettings)

## End(Not run)

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