normDotProduct: Normalized Dot Product

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

Normalized Dot Product

Description

This function calculates the similarity of all pairs of peaks from 2 samples, using the spectra similarity

Usage

normDotProduct(
  x1,
  x2,
  t1 = NULL,
  t2 = NULL,
  df = max(ncol(x1), ncol(x2)),
  D = 1e+05,
  timedf = NULL,
  verbose = FALSE
)

Arguments

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 NULL, 0 is used.
verbose	logical, whether to print out information

Details

Efficiently computes the normalized dot product between every pair of peak vectors and returns a similarity matrix. C code is called.

Value

matrix of similarities

Author(s)

Mark Robinson

References

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

See Also

dp, peaksAlignment

Examples

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]])

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