deter.iso: Generating list of type iso from filtered m/z differences.

In blosloos/nontarget: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data

Generating list of type iso from filtered m/z differences.

Description

Produces a list of m/z differences from diffs output generated by plotdiff to be used as argument iso in pattern.search. Thus, replaces the iso argument to pattern.search from make.isos and isotopes by another iso argument of the most frequent m/z differences detected among the HRMS peaks by plotdiff.

Usage

deter.iso(diffs, histbreaks = 50000, mzmin = 0, mzmax = 0.5, 
cutcount = 180, plotit = TRUE)

Arguments

diffs	vector diffs, i.e. output of function plotdiff
histbreaks	Number of histogram breaks; thus defines the mztol window to be used with pattern.search, see details.
mzmin	Minimum value for m/z differences in resulting iso list.
mzmax	Maximum value for m/z differences in resulting iso list.
cutcount	Histogram classes with frequencies below cutcount will be excluded from iso
plotit	Should a plot of the sekected histogram classes be plotted? Recommended.

Details

In addition to returning a iso argument, prints argument values for mztol, ppm and deter of pattern.search when using iso from deter.iso. Also see deter argument of pattern.search.

Value

List of type iso with 5 entries

iso[[1]]	"list of isotopes".
iso[[2]]	"list of isotope masses".
iso[[3]]	"charges".
iso[[4]]	"number of isotope m/z".
iso[[5]]	"elements".

Note

Experimental. For more consistent results, use make.isos instead.

Author(s)

Martin Loos

See Also

pattern.search plotdiff make.isos

Examples

data(peaklist)
diffs<-plotdiff(peaklist, histbreaks = 10000, rttol = c(0, 0), mztol = c(0.3, 100), plotit = TRUE);
iso<-deter.iso(diffs,histbreaks=10000,mzmin=0,mzmax=40,cutcount=500,plotit=TRUE);
pattern<-pattern.search(
  peaklist,
  iso,
  cutint=10000,
  rttol=c(-0.05,0.05),
  mztol=0.005,
  mzfrac=0.1,
  ppm=FALSE,
  inttol=0.2,
  #rules=c(FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE),
  rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
  deter=TRUE,
  entry=50
);

blosloos/nontarget documentation built on June 2, 2022, 3:53 p.m.