Man pages for cz-ye/DECENT
Differential Expression with Capture Efficiency adjustmeNT
| calc2DOProb | Calculate probability for dropout model |
| calc2NBProb | Calculate probability for negative binomial model |
| calc2PoisProb | Calculate probability for Poisson model |
| calcDOProb | Calculate probability for dropout model |
| calcNBProb | Calculate probability for negative binomial model |
| cbbinom.logl | Cost function for optimizing tau for spike-in data |
| dBBNB | Probablity mass function of the distribution for observed... |
| dbetabinom2 | dbetabinom function for non-integer input |
| dbinom2 | dbinom function for non-integer input |
| decent | DECENT |
| dnbinom2 | dnbinom function for non-integer input |
| dpois2 | dpois function for non-integer output |
| draw.sample | Draw one sample from the given distribution |
| Estep2ByGene | E-step with Gauss–Legendre quadrature approximation |
| EstepByGene | E-step without Gauss–Legendre quadrature approximation |
| fitNoDE | Fitting the unrestricted model with EM algorithm |
| getImputed | Get imputed data |
| getSImputed | Get imputed data |
| loglI | Calculate Log Likelihood |
| loglI2 | Calculate Log Likelihood |
| loglI.GQ | Calculate Log Likelihood of Incomplete Data |
| lrTest | Likelihood-ratio test |
| MstepNB | M-step |
| sim | Simulated data |
| SImputeByGene | Perform single imputation for one gene using the fitted model |
| update.rho | Cost function for optimizing tau using endogenous genes |
| update.rho3 | Cost function for optimizing tau using endogenous genes |
| zinbGrad | Gradient of complete data log-likelihood function for DECENT... |
