SMASH (version 1.0.0)

grid_ITH_optim: 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
)

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.

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