corPrt: Retention Time Penalized Correlation

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

Retention Time Penalized Correlation

Description

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

Usage

corPrt(d1, d2, t1, t2, D, penality = 0.2)

Arguments

d1	data matrix for sample 1
d2	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
penality	penalization applied to the matching between two mass spectra if (t1-t2)>D

Details

Computes the Pearson carrelation between every pair of peak vectors in the retention time window (D)and returns the 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 <- corPrt(data@peaksdata[[1]], data@peaksdata[[2]],
           data@peaksrt[[1]], data@peaksrt[[2]], D = 50, penality = 0.2)
## End (Not Run)

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