xcms (version 1.48.0)

specDist-methods: Distance methods for xcmsSet, xcmsRaw and xsAnnotate

Description

There are several methods for calculating a distance between two sets of peaks in xcms. specDist is the generic method.

Arguments

object

a xcmsSet or xcmsRaw.

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

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.