ISOpure.calculate.tac   Perform calculation for Tumour Adjacent Cell
                        (TAC) profiles
ISOpure.model_optimize.cg_code.rminimize
                        Minimize a differentiable multivariate function
ISOpure.model_optimize.vv.vv_deriv_loglikelihood
                        Compute the derivative of the loglikelihood
                        relevant to vv for step 1
ISOpure.model_optimize.vv.vv_loglikelihood
                        Compute the loglikelihood relevant to vv for
                        step 1
ISOpure.step1.CPE       Perform first step of ISOpure purification
                        algorithm
ISOpure.step2.PPE       Perform second step of ISOpure purification
                        algorithm
ISOpure.util.logsum     Log-sum-exp
ISOpure.util.matlab_greater_than
                        Greater than operator
ISOpure.util.matlab_less_than
                        Less than operator
ISOpure.util.matlab_log
                        Modified logarithm function
ISOpure.util.repmat     Tiles matrix horizontally or vertically
ISOpureS1.model_core.compute_loglikelihood
                        Compute loglikelihood given all model
                        parameters for step 1
ISOpureS1.model_core.new_model
                        Initialize a model list to hold all the
                        parameters
ISOpureS1.model_core.optmodel
                        Optimizes the ISOpure parameters for step 1
ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood
                        Compute loglikelihood relevant to kappa for
                        step 1
ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood
                        Compute derivative of loglikelihood with
                        respect to kappa for step 1
ISOpureS1.model_optimize.kappa.kappa_loglikelihood
                        Compute loglikelihood relevant to kappa for
                        step 1
ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood
                        Compute the derivative of the loglikelihood
                        relevant to mm for step 1
ISOpureS1.model_optimize.mm.mm_loglikelihood
                        Compute the loglikelihood relevant to mm for
                        step 1
ISOpureS1.model_optimize.omega.omega_compute_loglikelihood
                        Compute loglikelihood relevant to omega for
                        step 1
ISOpureS1.model_optimize.omega.omega_deriv_loglikelihood
                        Compute the derivative of loglikelihood
                        relevant to omega for step 1
ISOpureS1.model_optimize.omega.omega_loglikelihood
                        Compute the loglikelihood relevant to omega for
                        step 1
ISOpureS1.model_optimize.opt_kappa
                        Optimize kappa in step 1
ISOpureS1.model_optimize.opt_mm
                        Optimize the reference cancer profile, m, in
                        step 1
ISOpureS1.model_optimize.opt_omega
                        Optimize omega in step 1
ISOpureS1.model_optimize.opt_theta
                        Optimize theta in step 1
ISOpureS1.model_optimize.opt_vv
                        Optimize vv in step 1
ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood
                        Compute the derivative of loglikelihood
                        relevant to theta for step 1
ISOpureS1.model_optimize.theta.theta_loglikelihood
                        Compute the loglikelihood relevant to theta for
                        step 1
ISOpureS1.model_optimize.vv.vv_compute_loglikelihood
                        Compute loglikelihood relevant to vv for step 1
ISOpureS2.model_core.compute_loglikelihood
                        Compute loglikelihood given all model
                        parameters for step 2
ISOpureS2.model_core.new_model
                        Compute loglikelihood given all model
                        parameters for step 2
ISOpureS2.model_core.optmodel
                        Optimizes the ISOpure parameters for step 2
ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood
                        Compute the derivative of loglikelihood
                        relevant to the patient cancer profiles, cc,
                        for step 2
ISOpureS2.model_optimize.cc.cc_loglikelihood
                        Compute the loglikelihood relevant to the
                        patient cancer profiles, cc, for step 2
ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihood
                        Compute loglikelihood relevant to kappa for
                        step 2
ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood
                        Compute derivative of loglikelihood with
                        respect to kappa for step 2
ISOpureS2.model_optimize.kappa.kappa_loglikelihood
                        Compute loglikelihood relevant to kappa for
                        step 2
ISOpureS2.model_optimize.opt_cc
                        Optimize the tumor-specific cancer profiles in
                        step 2
ISOpureS2.model_optimize.opt_kappa
                        Optimize kappa in step 2
ISOpureS2.model_optimize.opt_theta
                        Optimize theta in step 2
ISOpureS2.model_optimize.opt_vv
                        Optimize vv in step 2
ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood
                        Compute the derivative of loglikelihood
                        relevant to theta for step 2
ISOpureS2.model_optimize.theta.theta_loglikelihood
                        Compute the loglikelihood relevant to theta for
                        step 2
ISOpureS2.model_optimize.vv.vv_compute_loglikelihood
                        Compute loglikelihood relevant to vv for step 2
