ISOpureS1.model_optimize.kappa.kappa_loglikelihood {ISOpureR}

Compute loglikelihood relevant to kappa for step 1

Description

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.

Usage

ISOpureS1.model_optimize.kappa.kappa_loglikelihood(log_kappa, tumordata, model)

Arguments

log_kappa

the scalar log(kappa - model\$MIN_KAPPA)

tumordata

a GxD matrix representing gene expression profiles of tumour samples

model

list containing all the parameters to be optimized

Value

The negative of the loglikelihood relevant to optimizing kappa

Author(s)

Gerald Quon, Catalina Anghel, Francis Nguyen