specDist-methods {xcms} | R Documentation

## 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.

### 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`.

### 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,...)`

### Author(s)

Joachim Kutzera, jkutzer@ipb-halle.de

[Package xcms version 3.2.0 Index]