dynRT: dynRT

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

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)

[e-mail]

Examples

require(gcspikelite)
files <- list.files(path = paste(find.package("gcspikelite"), "data",
                    sep = "/"),"CDF", full = TRUE)
data <- peaksDataset(files[1:2], mz = seq(50, 550), rtrange = c(7.5, 8.5))
## create settings object
mfp <- xcms::MatchedFilterParam(fwhm = 10, snthresh = 5)
cwt <- xcms::CentWaveParam()
data <- addXCMSPeaks(files[1:2], data, settings = mfp, multipleMF = FALSE)
data
## review peak picking
plotChrom(data, rtrange=c(7.5, 10.5), runs=c(1:2))
## similarity
r <- ndpRT(data@peaksdata[[1]], data@peaksdata[[2]], data@peaksrt[[1]],
    data@peaksrt[[2]], D = 50)
## dynamic retention time based alignment algorithm
v <- dynRT(S = r)

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.