Description Usage Arguments Value Examples
The parameters of the model given as argument are optimized by penalized maximum likelihood on the count matrix given as argument. It is recommended to call zinb_initialize before this function to have good starting point for optimization, since the optimization problem is not convex and can only converge to a local minimum.
1 2 3 4 5 6 7 8 9 | zinbOptimize(
m,
Y,
commondispersion = TRUE,
maxiter = 25,
stop.epsilon = 1e-04,
verbose = FALSE,
BPPARAM = BiocParallel::bpparam()
)
|
m |
The model of class ZinbModel |
Y |
The matrix of counts. |
commondispersion |
Whether the dispersion is the same for all features (default=TRUE) |
maxiter |
maximum number of iterations (default 25) |
stop.epsilon |
stopping criterion, when the relative gain in likelihood is below epsilon (default 0.0001) |
verbose |
print information (default FALSE) |
BPPARAM |
object of class |
An object of class ZinbModel similar to the one given as argument with modified parameters alpha_mu, alpha_pi, beta_mu, beta_pi, gamma_mu, gamma_pi, W.
1 2 3 4 | Y = matrix(10, 3, 5)
m = zinbModel(n=NROW(Y), J=NCOL(Y))
m = zinbInitialize(m, Y, BPPARAM=BiocParallel::SerialParam())
m = zinbOptimize(m, Y, BPPARAM=BiocParallel::SerialParam())
|
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