Prefit Poisson MASH Model without DE Effects — pois_mash

Prefit the poisson mash model to get an initial estimate of model parameters including mu, psi2 and rho.

pois_mash_prefit(
  data,
  ruv = FALSE,
  Fuv,
  update.mu = TRUE,
  verbose = FALSE,
  init = list(),
  control = list()
)

pois_mash_prefit_control_default()

Arguments

data: “pois.mash” data object, typically created by calling pois_mash_set_data.
ruv: Logical scalar indicating whether to account for unwanted variation. If ruv = TRUE, Fuv must be provided.
Fuv: J x D matrix of latent factors causing unwanted variation, with features as rows and latent factors as columns.
update.mu: A logical scalar indicating whether to update gene-specific means mu. If update.mu = FALSE, initial mu must be provided in init.
verbose: Logical scalar indicating whether to print ELBO at each iteration.
init: List of initial values for model parameters which could be empty.
control: List of control parameters with one or more of the following elements: “maxiter”, maximum number of iterations; “maxiter.q”, maximum number of inner-loop iterations to update variational parameters at each iteration; “tol.stop”, tolerance for assessing convergence of prefit, as measured by absolute change in ELBO; “tol.q”, relative tolerance for assessing convergence of variational parameters at each iteration; “tol.rho”, tolerance for assessing convergence of effects corresponding to unwanted variation. Any named components will override the default optimization algorithm settings (as they are defined by pois_mash_ruv_prefit_control_default).

Value

A list containing initial estimates of model parameters.