get_initialization — get_initialization • tickTack

Perform c-means on the proportions of mutations that fall in to the first or second binomial interval (in accepted mutations) and retrieve the centroids and u matrix to be used as initialization parameters.

Usage

get_initialization(input_data, purity, phi = c(), kappa = 5, alpha = 0.05)

Arguments

input_data: list: List of 7: $S: int, $N: int, $karyotype: num (0 or 1), $seg_assignment: num, $peaks:List of N of num (1:2), $NV: num, $DP: num
purity: num: (type = double) sample purity between 0 and 1
phi: parameters of dirichlet reparametrization uniformly initialized
kappa: parameters of dirichlet reparametrization
alpha: num: (type double) confidence interval level to choose the data that fall in the expected binomial intervals

Value

inits list: List of 4: $w: num (1:S, 1:3), $tau: num (1:K), $phi: num (1:K), $kappa: num