Man pages for zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq Data
| computeDevianceResiduals | Deviance residuals of the zero-inflated negative binomial... |
| computeObservationalWeights | Observational weights of the zero-inflated negative binomial... |
| getAlpha_mu | Returns the matrix of paramters alpha_mu |
| getAlpha_pi | Returns the matrix of paramters alpha_pi |
| getBeta_mu | Returns the matrix of paramters beta_mu |
| getBeta_pi | Returns the matrix of paramters beta_pi |
| getEpsilon_alpha | Returns the vector of regularization parameter for alpha |
| getEpsilon_beta_mu | Returns the vector of regularization parameter for beta_mu |
| getEpsilon_beta_pi | Returns the vector of regularization parameter for beta_pi |
| getEpsilon_gamma_mu | Returns the vector of regularization parameter for gamma_mu |
| getEpsilon_gamma_pi | Returns the vector of regularization parameter for gamma_pi |
| getEpsilon_W | Returns the vector of regularization parameter for W |
| getEpsilon_zeta | Returns the regularization parameter for the dispersion... |
| getGamma_mu | Returns the matrix of paramters gamma_mu |
| getGamma_pi | Returns the matrix of paramters gamma_pi |
| getLogitPi | Returns the matrix of logit of probabilities of zero |
| getLogMu | Returns the matrix of logarithm of mean parameters |
| getMu | Returns the matrix of mean parameters |
| getPhi | Returns the vector of dispersion parameters |
| getPi | Returns the matrix of probabilities of zero |
| getTheta | Returns the vector of inverse dispersion parameters |
| getV_mu | Returns the gene-level design matrix for mu |
| getV_pi | Returns the gene-level design matrix for pi |
| getW | Returns the low-dimensional matrix of inferred sample-level... |
| getX_mu | Returns the sample-level design matrix for mu |
| getX_pi | Returns the sample-level design matrix for pi |
| getZeta | Returns the vector of log of inverse dispersion parameters |
| glmWeightedF | Zero-inflation adjusted statistical tests for assessing... |
| imputeZeros | Impute the zeros using the estimated parameters from the ZINB... |
| independentFiltering | Perform independent filtering in differential expression... |
| loglik | Compute the log-likelihood of a model given some data |
| nFactors | Generic function that returns the number of latent factors |
| nFeatures | Generic function that returns the number of features |
| nParams | Generic function that returns the total number of parameters... |
| nSamples | Generic function that returns the number of samples |
| orthogonalizeTraceNorm | Orthogonalize matrices to minimize trace norm of their... |
| penalty | Compute the penalty of a model |
| pvalueAdjustment | Perform independent filtering in differential expression... |
| solveRidgeRegression | Solve ridge regression or logistic regression problems |
| toydata | Toy dataset to check the model |
| zinbAIC | Compute the AIC of a model given some data |
| zinbBIC | Compute the BIC of a model given some data |
| zinbFit | Fit a ZINB regression model |
| zinbInitialize | Initialize the parameters of a ZINB regression model |
| zinb.loglik | Log-likelihood of the zero-inflated negative binomial model |
| zinb.loglik.dispersion | Log-likelihood of the zero-inflated negative binomial model,... |
| zinb.loglik.dispersion.gradient | Derivative of the log-likelihood of the zero-inflated... |
| zinb.loglik.matrix | Log-likelihood of the zero-inflated negative binomial model... |
| zinb.loglik.regression | Penalized log-likelihood of the ZINB regression model |
| zinb.loglik.regression.gradient | Gradient of the penalized log-likelihood of the ZINB... |
| zinbModel | Initialize an object of class ZinbModel |
| ZinbModel-class | Class ZinbModel |
| zinbOptimize | Optimize the parameters of a ZINB regression model |
| zinbOptimizeDispersion | Optimize the dispersion parameters of a ZINB regression model |
| zinb.regression.parseModel | Parse ZINB regression model |
| zinbSim | Simulate counts from a zero-inflated negative binomial model |
| zinbsurf | Perform dimensionality reduction using a ZINB regression... |
| zinbwave | Perform dimensionality reduction using a ZINB regression... |
