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,...)
Arguments
- object
a xcmsSet or xcmsRaw.
- method
Method to use for distance calculation. See details.
- ...
mzabs, mzppm and parameters for the distance function.
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