ISOpureS2.model_optimize.opt_kappa: Optimize kappa in step 2

In ISOpureR: Deconvolution of Tumour Profiles

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.step2.PPE.)

Usage

ISOpureS2.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 (which is a 1xD vector) updated

Author(s)

Gerald Quon, Catalina Anghel, Francis Nguyen

ISOpureR documentation built on May 11, 2019, 1:02 a.m.