calibrate: Calibrate peaks for correcting unprecise m/z values

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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,

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.