Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-methods.Rd
There are several methods for calculating a distance between two sets of peaks in xcms. specDist
is the generic method.
Methods
- object = "xcmsSet"
specDist(object, peakIDs1, peakIDs2,...)
- object = "xsAnnotate"
specDist(object, PSpec1, PSpec2,...)
Details
Different algorithms can be used by specifying them with the
method
argument. For example to use the "meanMZmatch"
approach with xcmsSet one would use:
specDist(object, peakIDs1, peakIDs2, method="meanMZmatch")
. This is also
the default.
Further arguments given by ...
are
passed through to the function implementing
the method
.
A character vector of nicknames for the
algorithms available is returned by
getOption("BioC")$xcms$specDist.methods
.
If the nickname of a method is called "meanMZmatch",
the help page for that specific method can
be accessed with ?specDist.meanMZmatch
.
Value
- mzabs
maximum absolute deviation for two matching peaks
- mzppm
relative deviations in ppm for two matching peaks
- symmetric
use symmetric pairwise m/z-matches only, or each match
Author
Joachim Kutzera, jkutzer@ipb-halle.de