R: Mass defect vs. m/z scatterplot of HRMS peaks, with specific...
plotdefect
R Documentation
Mass defect vs. m/z scatterplot of HRMS peaks, with specific m/z isotope differences highlighted.
Description
Mass defect vs. m/z scatterplot of HRMS peaks, with specific m/z isotope differences highlighted.
Usage
plotdefect(pattern, elements = c("Br"))
Arguments
pattern
List of type pattern produced by pattern.search.
elements
Character string of an element for which the isotope m/z differences between two peaks detected by pattern.search should be highlighted (red).
Note
Here, mass defect is defined as the difference of m/z to the nearest integer from rounding.
rm.comp = FALSE and rm.noncomp = FALSE leads to no selection and thus no exclusion of anything.
Author(s)
Martin Loos
See Also
pattern.search
Examples
data(peaklist);
peaklist<-rm.sat(peaklist,dmz=0.3,drt=0.1,intrat=0.015,spar=0.8,corcut=-1000,plotit=TRUE);
peaklist<-peaklist[peaklist[,4],1:3];
data(isotopes);
iso<-make.isos(isotopes,
use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2))
pattern<-pattern.search(
peaklist,
iso,
cutint=10000,
rttol=c(-0.05,0.05),
mztol=2,
mzfrac=0.1,
ppm=TRUE,
inttol=0.2,
rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
deter=FALSE,
entry=50
);
plotdefect(pattern,elements=c("N"));
plotdefect(pattern,elements=c("Cl"));
plotdefect(pattern,elements=c("Br"));
plotdefect(pattern,elements=c("S"));
plotdefect(pattern,elements=c("C"));
plotdefect(pattern,elements=c("K"));
# P has only one isotope, hence:
# plotdefect(pattern,elements=c("P"));