specDist-methods | R Documentation |
There are several methods for calculating a distance between two sets of peaks in xcms. specDist
is the generic method.
object |
a xcmsSet or xcmsRaw. |
method |
Method to use for distance calculation. See details. |
... |
mzabs, mzppm and parameters for the distance function. |
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
.
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 |
specDist(object, peakIDs1, peakIDs2,...)
specDist(object, PSpec1, PSpec2,...)
Joachim Kutzera, jkutzer@ipb-halle.de
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