lmmsde class a S4 class that extends lmms class.

Description

lmmsde class inherits from class lmms and extends it with six further slots: DE, model.time, model.group, model.time.group, type and experiment. The class lmmsde is returned when applying lmmsDE method.

Slots

DE

A data.frame returning p-values and adjusted p-values using Benjamini-Hochberg correction for multiple testing of the differential expression testing over time, group or their interaction.

modelsUsed

A list of lme, containing the models used to model the particular condition of interest.

predTime

A matrix returning the predicted time fit.

predGroup

A matrix returning the predicted group fit.

predTimeGroup

A matrix returning the predicted time group interaction fit.

modelTime

A list of classlme, containing the models for every molecule modelling the time effect.

modelGroup

A list of class lme, containing the models for every molecule modelling group effect.

modelTimeGroup

A list of class lme, containing the models for every molecule modelling time and group interaction effect.

type

An object of class character, describing the test performed.

experiment

An object of class character describing the model used to perform differential expression analysis.