corncob (version 0.4.1)

genInits: Generate initialization for optimization

Description

Generate initialization for optimization

Usage

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

Value

Matrix of initializations

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)

link

ink function for abundance covariates

phi.link

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.

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)