psDist-methods: Distance methods for xsAnnotate
In CAMERA: Collection of annotation related methods for mass spectrometry data

Description Arguments Details Value Methods Author(s)

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.

`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.

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.

`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