useDefaultFwhm: Use pre-computed default FWHM models

In CeMOS-Mannheim/moleculaR: Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging

Use pre-computed default FWHM models

Description

– this is still under development – – currently only 'constant' fwhm values could be provided –

Usage

useDefaultFwhm(userMassRes, modality = "FTICR", constant = FALSE)

Arguments

userMassRes:	a named vector of the form 'c(massRes= , mass= )' that specify user-provided mass resolution at a given m/z. This will used to adjust the height of the FWHM curve depending on the chosen 'modality'.
modality:	a character specifying the type of the MSI measurement device. Curretly only 'c("FTICR", "TOF-reflector", "TIMS-TOF")' are supported.
constant:	a logical, when set to 'TRUE', the fwhm value computed from 'userMassRes' is used for the entire mass range.

Details

This creates a linear interpolator function that approximats fwhm as a function of m/z for the given MSI modality.

The defaults are pre-computed and might not represent the true FWHM(m/z) curve for a given dataset. The user has the option to adjust the hight of the curve if the mass resolution value at a given m/z is provided. Alternatively, the user could simply provide a single FWHM value which will be used for the entire mass range. Note that this is not advised but provided (with a warning) for the user's convenience and for testing.

Value

Returns an S3 object 'fwhm' containing a linear interplotor function 'fwhmInterpolator' in addition to m/z values of the peaks and their corresponding fwhm values.

CeMOS-Mannheim/moleculaR documentation built on April 14, 2025, 8:27 a.m.