initialize_tau: initialize_tau

In sellerslab/gemini: GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

initialize_tau

Description

Initialize all tau values based on the observed replicate variance.

Usage

initialize_tau(
  Model,
  CONSTANT = 32,
  prior_shape = 0.5,
  window = NULL,
  monotonize = FALSE,
  verbose = FALSE
)

Arguments

Model	an object of class gemini.model
CONSTANT	a numeric indicating a constant value that shifts counts to reduce outliers (default = 32).
prior_shape	shape parameter of Gamma distribution used to model the variation in the data in Input. If single numeric value, then shape parameters for all samples are assumed equal. Otherwise, a named numeric vector of shape parameters the same length as the number of samples (excluding early time point).
window	numeric if window smoothing should be done on initialized tau values, otherwise NULL (default) for no window smoothing
monotonize	logical specifying whether the variance should be monotonically increasing (default FALSE)
verbose	default FALSE

Value

a Model object of class gemini.model including new slots for alpha and beta values

Examples

data("Model", package = "gemini")
Model <- initialize_tau(Model, CONSTANT = 32, prior_shape = 0.5)

sellerslab/gemini documentation built on Dec. 5, 2022, 8:56 a.m.