dynRT: dynRT
In flagme: Analysis of Metabolomics GC/MS Data

Description Usage Arguments Details Value Author(s) Examples

Dynamic Retention Time Based Alignment algorithm, given a similarity matrix

dynRT(S)

`S`	similarity matrix

This function align two chromatograms finding the maximum similarity among the mass spectra

list containing the matched peaks between the two chromatograms. The number represent position of the spectra in the S matrix

riccardo.romoli@unifi.it

require(gcspikelite)
gcmsPath <- paste(find.package("gcspikelite"), "data", sep="/")
cdfFiles <- dir(gcmsPath,"CDF", full=TRUE)
## read data, peak detection results
pd <- peaksDataset(cdfFiles[1:3], mz=seq(50,550),
    rtrange=c(7.5,10.5))
pd <- addXCMSPeaks(files=cdfFiles[1:3], object=pd,
    peakPicking=c('mF'),snthresh=3, fwhm=10,  step=0.1, steps=2,
    mzdiff=0.5, sleep=0)
## review peak picking
plot(pd, rtrange=c(7.5, 10.5), runs=c(1:3))
## similarity
r <- ndpRT(pd@peaksdata[[1]], pd@peaksdata[[2]], pd@peaksrt[[1]],
    pd@peaksrt[[2]], D=50)
## dynamic retention time based alignment algorithm
v <- dynRT(S=r)