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