corPrt: Retention Time Penalized Correlation
In flagme: Analysis of Metabolomics GC/MS Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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`

Computes the Pearson carrelation between every pair of peak vectors in the retention time window (D)and returns the similarity matrix.

matrix of similarities

Riccardo Romoli

peaksAlignment

## Not Run
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))

r <- corPrt(pd@peaksdata[[1]], pd@peaksdata[[2]],
           pd@peaksrt[[1]], pd@peaksrt[[2]], D=50, penality=0.2)
## End (Not Run)