calibrate-calibrant-mass: Calibrant mass based calibration of chromatgraphic peaks
In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

CalibrantMassParam-class

R Documentation

Calibrant mass based calibration of chromatgraphic peaks

Description

Calibrate peaks using mz values of known masses/calibrants. mz values of identified peaks are adjusted based on peaks that are close to the provided mz values. See details below for more information.

The isCalibrated function returns TRUE if chromatographic peaks of the XCMSnExp object x were calibrated and FALSE otherwise.

Usage

CalibrantMassParam(mz = list(), mzabs = 1e-04, mzppm = 5,
  neighbors = 3, method = "linear")

isCalibrated(object)

## S4 method for signature 'XCMSnExp'
calibrate(object, param)

Arguments

`mz`	a `numeric` or `list` of `numeric` vectors with reference mz values. If a `numeric` vector is provided, this is used for each sample in the `XCMSnExp` object. If a `list` is provided, it's length has to be equal to the number of samples in the experiment.
`mzabs`	`numeric(1)` the absolute error/deviation for matching peaks to calibrants (in Da).
`mzppm`	`numeric(1)` the relative error for matching peaks to calibrants in ppm (parts per million).
`neighbors`	`integer(1)` with the maximal number of peaks within the permitted distance to the calibrants that are considered. Among these the mz value of the peak with the largest intensity is used in the calibration function estimation.
`method`	`character(1)` defining the method that should be used to estimate the calibration function. Can be `"shift"`, `"linear"` (default) or `"edgeshift"`.
`object`	An XCMSnExp object.
`param`	The `CalibrantMassParam` object with the calibration settings.

Details

The method does first identify peaks that are close to the provided mz values and, given that there difference to the calibrants is smaller than the user provided cut off (based on arguments mzabs and mzppm), their mz values are replaced with the provided mz values. The mz values of all other peaks are either globally shifted (for method = "shift" or estimated by a linear model through all calibrants. Peaks are considered close to a calibrant mz if the difference between the calibrant and its mz is <= mzabs + mz * mzppm /1e6.

Adjustment methods: adjustment function/factor is estimated using the difference between calibrant and peak mz values only for peaks that are close enough to the calibrants. The availabel methods are:

shift: shifts the m/z of each peak by a global factor which corresponds to the average difference between peak mz and calibrant mz.
linear: fits a linear model throught the differences between calibrant and peak mz values and adjusts the mz values of all peaks using this.
edgeshift: performs same adjustment as linear for peaks that are within the mz range of the calibrants and shift outside of it.

For more information, details and examples refer to the xcms-direct-injection vignette.

Value

For CalibrantMassParam: a CalibrantMassParam instance. For calibrate: an XCMSnExp object with chromatographic peaks being calibrated. Be aware that the actual raw mz values are not (yet) calibrated, but only the identified chromatographic peaks.

The CalibrantMassParam function returns an instance of the CalibrantMassParam class with all settings and properties set.

The calibrate method returns an XCMSnExp object with the chromatographic peaks being calibrated. Note that only the detected peaks are calibrated, but not the individual mz values in each spectrum.