dynRT {flagme} | R Documentation |
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)