calibrate-methods {xcms} | R Documentation

## Calibrate peaks for correcting unprecise m/z values

### Description

Calibrate peaks of a xcmsSet via a set of known masses

### Arguments

`object` | a `xcmsSet` object with uncalibrated mz
`calibrants` | a vector or a list of vectors with reference m/z-values
`method` | the used calibrating-method, see below
`mzppm` | the relative error used for matching peaks in ppm (parts per million)
`mzabs` | the absolute error used for matching peaks in Da
`neighbours` | the number of neighbours from wich the one with the highest intensity is used (instead of the nearest)
`plotres` | can be set to TRUE if wanted a result-plot showing the found m/z with the distances and the regression

### Value

`object` | a `xcmsSet` with one ore more samples
`calibrants` | for each sample different calibrants can be used, if a list of m/z-vectors is given. The length of the list must be the same as the number of samples, alternatively a single vector of masses can be given which is used for all samples.
`method` | "shift" for shifting each m/z, "linear" does a linear regression and adds a linear term to each m/z. "edgeshift" does a linear regression within the range of the mz-calibrants and a shift outside.

### Methods

object = "xcmsSet"

  `calibrate(object, calibrants,method="linear", mzabs=0.0001, mzppm=5, neighbours=3, plotres=FALSE)`

### See Also

`xcmsSet-class`,

[Package xcms version 3.2.0 Index]