ParameterSet-class: An S4 class for defining DexBatch parameter ranges

In MPCary/DEXICA: Functions for predicting and validating gene modules

Description

A ParameterSet object defines a range of parameter values to test in a DexBatch (see DexBatch-class).

Usage

## Constructor:
parameterSet(n.comp = 1, center.cols = c(TRUE), scale.cols = c(FALSE),
center.rows = c(FALSE), scale.rows = c(FALSE),
alg.typ = "parallel", fun = "logcosh", alpha = 1,
maxit = 200, tol = 1e-04, w.init = NULL, max.attempts = 3, verbose = FALSE)

## S4 method for signature 'ParameterSet'
getParamSetCount(object)

## S4 method for signature 'ParameterSet'
getOneParamSet(object, j)

## S4 method for signature 'ParameterSet'
getAllParamSets(object)

## S4 method for signature 'ParameterSet'
reseedParamSets(object, new.seeds = NULL)

Details

When creating a DexBatch object, a ParameterSet may be supplied (in the params slot) in order to specify a range of parameter values to test. Each slot in ParameterSet may accept either a single value or a range of values. If multiple slots have multiple values, the ParameterSet will encompass each possible combination of individual slot values.

Any slot values not specified during object construction are given their default values (see constructor), e.g., calling parameterSet() results in a ParameterSet with a single set of parameter values. The getParamSetCount method returns the total number of parameter sets defined in a ParameterSet.

Methods (by generic)

• getParamSetCount: Get the number of parameter sets defined in a ParameterSet object (see getParamSetCount)

• getOneParamSet: Get a single parameter set defined in a ParameterSet object (see getOneParamSet)

• getAllParamSets: Get all parameter sets defined in a ParameterSet object (see getAllParamSets)

• reseedParamSets: Reset the random seeds in a ParameterSet object (see reseedParamSets)

Slots

n.comp

an integer or vector specifying the number of components to extract

alg.typ,fun,alpha,maxit,tol,w.init,max.attempts,verbose

See dexFastICA documentation

center.cols,scale.cols,center.rows,scale.rows,simultaneous

See preprocessMatrix documentation

MPCary/DEXICA documentation built on May 4, 2019, 2:35 p.m.