grid_ITH_optim: grid_ITH_optim

In Sun-lab/SMASH: Subclone Multiplicity Allocation and Somatic Heterogeneity

grid_ITH_optim

Description

This function performs a grid search over enumerated configurations within the pre-defined list eS

Usage

grid_ITH_optim(
  my_data,
  my_purity,
  list_eS,
  pi_eps0 = NULL,
  trials = 20,
  max_iter = 4000,
  my_epsilon = 1e-06
)

Arguments

my_data	A R dataframe containing the following columns: tAD tumor alternate read counts tRD tumor reference read counts CN_1 minor allele count CN_2 major allele count, where CN_1 <= CN_2 tCN CN_1 + CN_2
my_purity	A single numeric value of known/estimated purity
list_eS	A nested list of subclone configuration matrices
pi_eps0	A user-specified parameter denoting the proportion of loci not explained by the combinations of purity, copy number, multiplicity, and allocation. If NULL, it is initialized at 1e-3. If set to 0.0, the parameter is not estimated.
trials	Positive integer, number of random initializations of subclone proportions
max_iter	Positive integer, preferably 1000 or more, setting the maximum number of iterations
my_epsilon	Convergence criterion threshold for changes in the log likelihood, preferably 1e-6 or smaller

Value

A R list containing two objects. GRID is a dataframe where each row denotes a feasible subclone configuration with corresponding subclone proportion estimates q and somatic variant allocations alloc. INFER is a list where INFER[[i]] corresponds to the i-th row or model of GRID.

Sun-lab/SMASH documentation built on March 5, 2025, 8 p.m.