Man pages for zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq Data

computeDevianceResidualsDeviance residuals of the zero-inflated negative binomial...
computeObservationalWeightsObservational weights of the zero-inflated negative binomial...
getAlpha_muReturns the matrix of paramters alpha_mu
getAlpha_piReturns the matrix of paramters alpha_pi
getBeta_muReturns the matrix of paramters beta_mu
getBeta_piReturns the matrix of paramters beta_pi
getEpsilon_alphaReturns the vector of regularization parameter for alpha
getEpsilon_beta_muReturns the vector of regularization parameter for beta_mu
getEpsilon_beta_piReturns the vector of regularization parameter for beta_pi
getEpsilon_gamma_muReturns the vector of regularization parameter for gamma_mu
getEpsilon_gamma_piReturns the vector of regularization parameter for gamma_pi
getEpsilon_WReturns the vector of regularization parameter for W
getEpsilon_zetaReturns the regularization parameter for the dispersion...
getGamma_muReturns the matrix of paramters gamma_mu
getGamma_piReturns the matrix of paramters gamma_pi
getLogitPiReturns the matrix of logit of probabilities of zero
getLogMuReturns the matrix of logarithm of mean parameters
getMuReturns the matrix of mean parameters
getPhiReturns the vector of dispersion parameters
getPiReturns the matrix of probabilities of zero
getThetaReturns the vector of inverse dispersion parameters
getV_muReturns the gene-level design matrix for mu
getV_piReturns the gene-level design matrix for pi
getWReturns the low-dimensional matrix of inferred sample-level...
getX_muReturns the sample-level design matrix for mu
getX_piReturns the sample-level design matrix for pi
getZetaReturns the vector of log of inverse dispersion parameters
glmWeightedFZero-inflation adjusted statistical tests for assessing...
imputeZerosImpute the zeros using the estimated parameters from the ZINB...
independentFilteringPerform independent filtering in differential expression...
loglikCompute the log-likelihood of a model given some data
nFactorsGeneric function that returns the number of latent factors
nFeaturesGeneric function that returns the number of features
nParamsGeneric function that returns the total number of parameters...
nSamplesGeneric function that returns the number of samples
orthogonalizeTraceNormOrthogonalize matrices to minimize trace norm of their...
penaltyCompute the penalty of a model
pvalueAdjustmentPerform independent filtering in differential expression...
solveRidgeRegressionSolve ridge regression or logistic regression problems
toydataToy dataset to check the model
zinbAICCompute the AIC of a model given some data
zinbBICCompute the BIC of a model given some data
zinbFitFit a ZINB regression model
zinbInitializeInitialize the parameters of a ZINB regression model
zinb.loglikLog-likelihood of the zero-inflated negative binomial model
zinb.loglik.dispersionLog-likelihood of the zero-inflated negative binomial model,...
zinb.loglik.dispersion.gradientDerivative of the log-likelihood of the zero-inflated...
zinb.loglik.matrixLog-likelihood of the zero-inflated negative binomial model...
zinb.loglik.regressionPenalized log-likelihood of the ZINB regression model
zinb.loglik.regression.gradientGradient of the penalized log-likelihood of the ZINB...
zinbModelInitialize an object of class ZinbModel
ZinbModel-classClass ZinbModel
zinbOptimizeOptimize the parameters of a ZINB regression model
zinbOptimizeDispersionOptimize the dispersion parameters of a ZINB regression model
zinb.regression.parseModelParse ZINB regression model
zinbSimSimulate counts from a zero-inflated negative binomial model
zinbwavePerform dimensionality reduction using a ZINB regression...
zinbwave documentation built on Nov. 17, 2017, 1:56 p.m.