psDist-methods: Distance methods for xsAnnotate

Description

The package xcms contains several methods for calculating a distance between two sets of peaks. the CAMERA method psDist is the generic wrapper to use these methods for processing two pseudospectra from two different xsAnnotate objects.

Arguments

object1

a xsAnnotate object with pseudospectra

object2

a xsAnnotate object with pseudospectra

PSpec1

index of pseudospectrum in object1

PSpec2

index of pseudospectrum in object2

method

method to use for distance calculation. See details.

...

mzabs, mzppm and parameters for the distance function.

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

Methods

object1 = "xsAnnotate": specDist(object1, object2, pspectrum1, pspectrum2, method,...)

Details

Different algorithms can be used by specifying them with the method argument. For example to use the "meanMZmatch" approach one would use: specDist(object1, object2, pspectrum1, pspectrum2, 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 all the algorithms which are 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.