ISOpureS2.model_optimize.opt_vv {ISOpureR}

Optimize vv in step 2

Description

This function optimizes vv, the strength parameter in the prior over the reference cancer profile. Note that we don't directly optimize vv because it has constraints (must be >=1 to guarantee real-valued likelihoods).

Usage

ISOpureS2.model_optimize.opt_vv(
	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 vv parameter updated

Author(s)

Gerald Quon, Catalina Anghel, Francis Nguyen