ISOpureS1.model_optimize.kappa.kappa_loglikelihood function

Compute loglikelihood relevant to kappa for step 1

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.

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

Returns

The negative of the loglikelihood relevant to optimizing kappa

Author(s)

Gerald Quon, Catalina Anghel, Francis Nguyen