psDist-methods {CAMERA} | R Documentation

## 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.

### 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`.

### 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,...)`

### Author(s)

Joachim Kutzera, jkutzer@ipb-halle.de

[Package CAMERA version 1.42.0 Index]