Man pages for ISOpureR
Deconvolution of Tumour Profiles

ISOpure.calculate.tacPerform calculation for Tumour Adjacent Cell (TAC) profiles
ISOpure.model_optimize.cg_code.rminimizeMinimize a differentiable multivariate function
ISOpure.model_optimize.vv.vv_deriv_loglikelihoodCompute the derivative of the loglikelihood relevant to vv...
ISOpure.model_optimize.vv.vv_loglikelihoodCompute the loglikelihood relevant to vv for step 1
ISOpureS1.model_core.compute_loglikelihoodCompute loglikelihood given all model parameters for step 1
ISOpureS1.model_core.new_modelInitialize a model list to hold all the parameters
ISOpureS1.model_core.optmodelOptimizes the ISOpure parameters for step 1
ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihoodCompute loglikelihood relevant to kappa for step 1
ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihoodCompute derivative of loglikelihood with respect to kappa for...
ISOpureS1.model_optimize.kappa.kappa_loglikelihoodCompute loglikelihood relevant to kappa for step 1
ISOpureS1.model_optimize.mm.mm_deriv_loglikelihoodCompute the derivative of the loglikelihood relevant to mm...
ISOpureS1.model_optimize.mm.mm_loglikelihoodCompute the loglikelihood relevant to mm for step 1
ISOpureS1.model_optimize.omega.omega_compute_loglikelihoodCompute loglikelihood relevant to omega for step 1
ISOpureS1.model_optimize.omega.omega_deriv_loglikelihoodCompute the derivative of loglikelihood relevant to omega for...
ISOpureS1.model_optimize.omega.omega_loglikelihoodCompute the loglikelihood relevant to omega for step 1
ISOpureS1.model_optimize.opt_kappaOptimize kappa in step 1
ISOpureS1.model_optimize.opt_mmOptimize the reference cancer profile, m, in step 1
ISOpureS1.model_optimize.opt_omegaOptimize omega in step 1
ISOpureS1.model_optimize.opt_thetaOptimize theta in step 1
ISOpureS1.model_optimize.opt_vvOptimize vv in step 1
ISOpureS1.model_optimize.theta.theta_deriv_loglikelihoodCompute the derivative of loglikelihood relevant to theta for...
ISOpureS1.model_optimize.theta.theta_loglikelihoodCompute the loglikelihood relevant to theta for step 1
ISOpureS1.model_optimize.vv.vv_compute_loglikelihoodCompute loglikelihood relevant to vv for step 1
ISOpureS2.model_core.compute_loglikelihoodCompute loglikelihood given all model parameters for step 2
ISOpureS2.model_core.new_modelCompute loglikelihood given all model parameters for step 2
ISOpureS2.model_core.optmodelOptimizes the ISOpure parameters for step 2
ISOpureS2.model_optimize.cc.cc_deriv_loglikelihoodCompute the derivative of loglikelihood relevant to the...
ISOpureS2.model_optimize.cc.cc_loglikelihoodCompute the loglikelihood relevant to the patient cancer...
ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihoodCompute loglikelihood relevant to kappa for step 2
ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihoodCompute derivative of loglikelihood with respect to kappa for...
ISOpureS2.model_optimize.kappa.kappa_loglikelihoodCompute loglikelihood relevant to kappa for step 2
ISOpureS2.model_optimize.opt_ccOptimize the tumor-specific cancer profiles in step 2
ISOpureS2.model_optimize.opt_kappaOptimize kappa in step 2
ISOpureS2.model_optimize.opt_thetaOptimize theta in step 2
ISOpureS2.model_optimize.opt_vvOptimize vv in step 2
ISOpureS2.model_optimize.theta.theta_deriv_loglikelihoodCompute the derivative of loglikelihood relevant to theta for...
ISOpureS2.model_optimize.theta.theta_loglikelihoodCompute the loglikelihood relevant to theta for step 2
ISOpureS2.model_optimize.vv.vv_compute_loglikelihoodCompute loglikelihood relevant to vv for step 2
ISOpure.step1.CPEPerform first step of ISOpure purification algorithm
ISOpure.step2.PPEPerform second step of ISOpure purification algorithm
ISOpure.util.logsumLog-sum-exp
ISOpure.util.matlab_greater_thanGreater than operator
ISOpure.util.matlab_less_thanLess than operator
ISOpure.util.matlab_logModified logarithm function
ISOpure.util.repmatTiles matrix horizontally or vertically
ISOpureR documentation built on May 2, 2018, 1:04 a.m.