addAMDISPeaks: Add AMDIS peak detection results

In flagme: Analysis of Metabolomics GC/MS Data

Description

Reads ASCII ELU-format files (output from AMDIS) and attaches them to an already created peaksDataset object

Usage

addAMDISPeaks(object,fns=dir(,"[Eu][Ll][Uu]"),verbose=TRUE,...)

Arguments

object	a peaksDataset object.
fns	character vector of same length as object@rawdata (user ensures the order matches)
verbose	whether to give verbose output, default TRUE
...	arguments passed on to parseELU

Details

Repeated calls to parseELU to add peak detection results to the original peaksDataset object.

Value

peaksDataset object

Author(s)

Mark Robinson

References

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

See Also

parseELU, peaksDataset

Examples

# need access to CDF (raw data) and ELU files 
require(gcspikelite)
gcmsPath<-paste(find.package("gcspikelite"),"data",sep="/")

# full paths to file names
cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
eluFiles<-dir(gcmsPath,"ELU",full=TRUE)

# create a 'peaksDataset' object and add AMDIS peaks to it
pd<-peaksDataset(cdfFiles[1],mz=seq(50,550),rtrange=c(7.5,8.5))
pd<-addAMDISPeaks(pd,eluFiles[1])

flagme documentation built on Nov. 8, 2020, 5:24 p.m.