normDotProduct {flagme} | R Documentation |
This function calculates the similarity of all pairs of peaks from 2 samples, using the spectra similarity
normDotProduct(x1,x2,t1=NULL,t2=NULL,df=max(ncol(x1),ncol(x2)),D=100000,timedf=NULL,verbose=FALSE)
x1 |
data matrix for sample 1 |
x2 |
data matrix for sample 2 |
t1 |
vector of retention times for sample 1 |
t2 |
vector of retention times for sample 2 |
df |
distance from diagonal to calculate similarity |
D |
retention time penalty |
timedf |
matrix of time differences to normalize to. if |
verbose |
logical, whether to print out information |
Efficiently computes the normalized dot product between every pair of peak vectors and returns a similarity matrix. C code is called.
matrix of similarities
Mark Robinson
Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.
require(gcspikelite) # paths and files gcmsPath<-paste(find.package("gcspikelite"),"data",sep="/") cdfFiles<-dir(gcmsPath,"CDF",full=TRUE) eluFiles<-dir(gcmsPath,"ELU",full=TRUE) # read data, peak detection results pd<-peaksDataset(cdfFiles[1:2],mz=seq(50,550),rtrange=c(7.5,8.5)) pd<-addAMDISPeaks(pd,eluFiles[1:2]) r<-normDotProduct(pd@peaksdata[[1]],pd@peaksdata[[2]])