initialize_tau: initialize_tau

Description Usage Arguments Value Examples

View source: R/initialize_tau.R

Description

Initialize all tau values based on the observed replicate variance.

Usage

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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

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

sellerslab/gemini documentation built on April 9, 2021, 9:01 p.m.