ndpRT: Retention Time Penalized Normalized Dot Product

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

Retention Time Penalized Normalized Dot Product

Description

This function calculates the similarity of all pairs of peaks from 2 samples, using the spectra similarity and the retention time differencies

Usage

ndpRT(s1, s2, t1, t2, D)

Arguments

s1	data matrix for sample 1
s2	data matrix for sample 2
t1	vector of retention times for sample 1
t2	vector of retention times for sample 2
D	retention time window for the matching

Details

Computes the normalized dot product between every pair of peak vectors in the retention time window (D)and returns a similarity matrix.

Value

matrix of similarities

Author(s)

Riccardo Romoli

See Also

peaksAlignment

Examples

## Not Run
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))

r <- ndpRT(data@peaksdata[[1]], data@peaksdata[[2]],
           data@peaksrt[[1]], data@peaksrt[[2]], D = 50)
## End (Not Run)

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