ISOpureS1.model_optimize.kappa.kappa_loglikelihood

log_kappa

a GxD matrix representing gene expression profiles of tumour samples

tumordata

list containing all the parameters to be optimized

model

Computes the part of the loglikelihood function relevant to optimizing kappa for step 1. 
	Instead of performing constrained optimization on kappa directly, we optimize the log of kappa
   	in an unconstrained fashion.

math

Deconvolution of mixed tumour profiles into normal and cancer for each patient, using
the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires
mixed tumour profiles and a set of unmatched "basis" normal profiles.

ISOpureS1.model_optimize.kappa.kappa_loglikelihood: Compute loglikelihood relevant to kappa for step 1

Description

Usage

Arguments

Value