GenoGAM class

Description

This class is designed to represent the model object containing the estimate parameters, arguments and finals fits of the model on a basepair level.

Slots

design

A mgcv-type formula object.

fits

A data.frame of the fits, the standard error and the first and second derivative of the fits for each experiment.

positions

A GPos object of the positions and seqnames corresponding to the rows in the 'fits' slot.

smooths

A data.frame of knot positions and base function coefficients, in order to reproduce the splines and compute derivatives.

vcov

A list of covariance matrices for each tile fit.

experimentDesign

The design matrix according to which the fitting was performed.

fitparams

Global parameters 'lambda', 'theta', 'Coefficient of Variation' and the 'penalty order' used to compute the model.

family

The distribution family.

cvparams

Parameters used for cross validation.

settings

The global and local settings that were used to compute the model.

tileSettings

A list of settings used to compute tiles.

Author(s)

Georg Stricker georg.stricker@in.tum.de