# Deconvolution of Tumour Profiles

## Documentation for package ‘ISOpureR’ version 1.1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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