findPeaks-methods {xcms} | R Documentation

## Feature detection for GC/MS and LC/MS Data - methods

### Description

A number of peak pickers exist in XCMS. `findPeaks` is the generic method.

### Arguments

`object` | `xcmsRaw-class` object
`method` | Method to use for peak detection. See details.
`...` | Optional arguments to be passed along

### Details

Different algorithms can be used by specifying them with the `method` argument. For example to use the matched filter approach described by Smith et al (2006) one would use: `findPeaks(object, method="matchedFilter")`. 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")$xcms$findPeaks.methods`. If the nickname of a method is called "centWave", the help page for that specific method can be accessed with `?findPeaks.centWave`.

### Value

A matrix with columns:

`mz` | weighted (by intensity) mean of peak m/z across scans
`mzmin` | m/z of minimum step
`mzmax` | m/z of maximum step
`rt` | retention time of peak midpoint
`rtmin` | leading edge of peak retention time
`rtmax` | trailing edge of peak retention time
`into` | integrated area of original (raw) peak
`maxo` | maximum intensity of original (raw) peak

and additional columns depending on the choosen method.

### Methods

object = "xcmsRaw"

  `findPeaks(object, ...)`

### See Also

`findPeaks.matchedFilter` `findPeaks.centWave` `findPeaks.addPredictedIsotopeFeatures` `findPeaks.centWaveWithPredictedIsotopeROIs` `xcmsRaw-class`

[Package xcms version 3.10.2 Index]