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Generate initialization for optimization

Source: R/genInits.R
genInits.Rd

Generate initialization for optimization

Usage

genInits(W, M, X, X_star, np, npstar, link, phi.link, nstart = 1, use = TRUE)

Arguments

W

Numeric vector of counts

M

Numeric vector of sequencing depth

X

Matrix of covariates associated with abundance (including intercept)

X_star

Matrix of covariates associated with dispersion (including intercept)

np

Number of covariates associated with abundance (including intercept)

npstar

Number of covariates associated with dispersion (including intercept)

ink function for abundance covariates

ink function for dispersion covariates

nstart

Integer. Defaults to 1. Number of starts for optimization.

use

Boolean. Defaults to TRUE. Indicator of whether to use deterministic intialization.

Value

Matrix of initializations

Examples

set.seed(1)
seq_depth <- rpois(20, lambda = 10000)
my_counts <- rbinom(20, size = seq_depth, prob = 0.001) * 10
my_covariate <- cbind(rep(c(0,1), each = 10))
colnames(my_covariate) <- c("X1")

genInits(W = my_counts, M = seq_depth,
       X = cbind(1, my_covariate), X_star = cbind(1, my_covariate),
       np = 2, npstar = 2,
       link = "logit",
       phi.link = "logit", nstart = 2, use = TRUE)
#>                        X1                    
#> [1,] -4.669910 0.03427153  0.0000000 0.000000
#> [2,] -4.381932 0.28231162 -0.1073783 0.309576