newmodel-class {NewWave}R Documentation

Class newmodel

Description

Objects of this class store all the values needed to work with a negative binomial model, as described in the vignette. They contain all information to fit a model by penalized maximum likelihood or simulate data from a model.

Usage

## S4 method for signature 'newmodel'
show(object)

## S4 method for signature 'newmodel'
numberSamples(x)

## S4 method for signature 'newmodel'
numberFeatures(x)

## S4 method for signature 'newmodel'
numberFactors(x)

## S4 method for signature 'newmodel'
newX(object)

## S4 method for signature 'newmodel'
newV(object)

## S4 method for signature 'newmodel'
newLogMu(object)

## S4 method for signature 'newmodel'
newMu(object)

## S4 method for signature 'newmodel'
newZeta(object)

## S4 method for signature 'newmodel'
newPhi(object)

## S4 method for signature 'newmodel'
newTheta(object)

## S4 method for signature 'newmodel'
newEpsilon_beta(object)

## S4 method for signature 'newmodel'
newEpsilon_gamma(object)

## S4 method for signature 'newmodel'
newEpsilon_W(object)

## S4 method for signature 'newmodel'
newEpsilon_alpha(object)

## S4 method for signature 'newmodel'
newEpsilon_zeta(object)

## S4 method for signature 'newmodel'
newW(object)

## S4 method for signature 'newmodel'
newBeta(object)

## S4 method for signature 'newmodel'
newGamma(object)

## S4 method for signature 'newmodel'
newAlpha(object)

Arguments

object

an object of class newmodel.

x

an object of class newmodel.

Details

For the full description of the model see the model vignette. Internally, the slots are checked so that the matrices are of the appropriate dimensions: in particular, X, O and W need to have n rows, V needs to have J rows, zeta must be of length J.

Value

numberSamples returns the number of samples; numberFeaturesreturns the number of features; numberFactors returns the number of latent factors.

Methods (by generic)

Slots

X

matrix. The design matrix containing sample-level covariates, one sample per row.

V

matrix. The design matrix containing gene-level covariates, one gene per row.

X_intercept

logical. TRUE if X contains an intercept.

V_intercept

logical. TRUE if V contains an intercept.

W

matrix. The factors of sample-level latent factors.

beta

matrix or NULL. The coefficients of X in the regression.

gamma

matrix or NULL. The coefficients of V in the regression.

alpha

matrix. The weight of sample-level latent factors.

zeta

numeric. A vector of log of inverse dispersion parameters.

epsilon_beta

nonnegative scalar. Regularization parameter for beta

epsilon_gamma

nonnegative scalar. Regularization parameter for gamma

epsilon_W

nonnegative scalar. Regularization parameter for W

epsilon_alpha

nonnegative scalar. Regularization parameter for alpha

epsilon_zeta

nonnegative scalar. Regularization parameter for zeta


[Package NewWave version 1.3.0 Index]