dynRT {flagme}R Documentation

dynRT

Description

Dynamic Retention Time Based Alignment algorithm, given a similarity matrix

Usage

dynRT(S)

Arguments

S

similarity matrix

Details

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

Value

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

Author(s)

riccardo.romoli@unifi.it

Examples

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)

[Package flagme version 1.46.0 Index]