densityFunction: Class '"densityFunction"'

In baySeq: Empirical Bayesian analysis of patterns of differential expression in count data

Description

This function fills the '@densityFunction' slot of a ‘countData’ object. It defines the distribution used to estimate posterior likelihoods, and associated values used in these calculations.

Objects from the Class

Objects can be created by calls of the form new("densityFunction", ...).

Slots

description:

A description of the distribution defined.

density:

A "function", defining the likelihood of a data array given observed data and hyperparameters.

initiatingValues:

A "list" of functions (may be supplied as numerics) that define initial values of numeric prior discovery.

equalOverReplicates:

A "logical", describing which of the hyperparameters are equally marginally distributed over all groups, and which are not.

lower:

A "function", required to define the lower limit of optimisation in the case where only one hyperparameter is *not* equally marginally distributed over all groups.

upper:

A "function", required to define the upper limit of optimisation, as for ‘lower’, above.

stratifyFunction:

An optional "function", used to stratify the data for more accurate prior estimation.

stratifyBreaks:

An optional "numeric", used to define the number of strata in a stratification.

nullFunction:

An optional "function" on the hyperparameters, used to generate a one-dimensional distribution which can be partitioned to identify ‘null’ data.

orderingFunction:

An optional "function" for ordering the data between groups of a model.

modifyNullPriors:

An optional "function" for modifying the priors for the ‘null’ data.

Methods

No methods defined with class "densityFunction" in the signature.

Author(s)

Thomas J. Hardcastle

Examples

showClass("densityFunction")

baySeq documentation built on Nov. 8, 2020, 5:43 p.m.