Calibrate peaks for correcting unprecise m/z values
calibrate.RdCalibrate peaks of a xcmsSet via a set of known masses
Methods
- object = "xcmsSet"
calibrate(object, calibrants,method="linear", mzabs=0.0001, mzppm=5, neighbours=3, plotres=FALSE)
Arguments
- object
a
xcmsSetobject 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
xcmsSetwith 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.