ISOpureS1.model_optimize.opt_kappa {ISOpureR}

Optimize kappa in step 1

Description

This function optimizes kappa, the strength parameter in the prior over the reference cancer profile. Note that we don't directly optimize kappa because it has constraints (must be greater than the minimum determined in ISOpure.step1.CPE.)

Usage

ISOpureS1.model_optimize.opt_kappa(
	tumordata, 
	model, 
	NUM_ITERATIONS_RMINIMIZE, 
	iter, 
	NUM_GRID_SEARCH_ITERATIONS
	) 

Arguments

tumordata

a GxD matrix representing gene expression profiles of tumour samples

model

list containing all the parameters to be optimized

NUM_ITERATIONS_RMINIMIZE

minimum number of iteration that the minimization algorithm runs

iter

the iteration number

NUM_GRID_SEARCH_ITERATIONS

number of times to try restarting with different initial values

Value

The model with the kappa parameter updated

Author(s)

Gerald Quon, Catalina Anghel, Francis Nguyen