corPrt {flagme} | R Documentation |
This function calculates the similarity of all pairs of peaks from 2 samples, using the spectra similarity and the rretention time differencies
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 |
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
## 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)