modelfit-class: "Modelfit"

In IPPD: Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching

Description

Object returned from a call to fitModelParameters.

Slots

model

The chosen model, either "Gaussian" or "EMG".

fitting

The mode of fitting which generated the object. Either "most_intense" or "model".

alphafunction

A function of m/z that computes an estimate for the EMG parameter alpha. See fitModelParameters for more detailed information on this parameter.

sigmafunction

A function of m/z that computes an estimate for the EMG parameter sigma. See fitModelParameters for more detailed information on this parameter.

mufunction

A function of m/z that computes an estimate for the EMG parameter mu. See fitModelParameters for more detailed information on this parameter.

peakfitresults

A matrix of five columns if model = "Gaussian" and of six columns if model = "EMG", respectively. The matrix contains basic information on the extracted peaks and the corresponding parameters. The first column contains the number of (mz, intensity)-pairs used for fitting, the second column contains the residual sums of squares of the model fit, the middle columns the parameter estimates and the last column the m/z position.

bestpeak

A list containing detailed information on the 'best' peak, where 'best' is equivalent to 'minimum residual sums of squares' after fitting. Mainly used indirectly by calling the function visualize.

Methods

show

Use show(object) for brief information about the object.

visualize

A function to display graphically the result of parameter estimation. One can either visualize a single peak (slot(object, "bestpeak")) or the fit of the linear models postulated for the parameters alpha, sigma and mu. The function visualize is called with the following set of parameters.

object

An object of class modelfit.

type

A character specifying the object to be visualized. If type = "peak", the fit of a single peak stored in object@bestpeak is displayed. If type = "model", one obtains scatterplots of the form parameter vs. mz for each parameter in parameters, s. below.

parameters

Needed if and only if type = "model" in order to choose the y-variable of the scatterplot. Several parameters may be specified at a time, in which case one obtains a multi-panel plot.

modelfit

A logical indicating whether the estimated regression functions should be added to the scatterplots (if type = "model").

IPPD documentation built on April 28, 2020, 6:58 p.m.