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ISOpureR (version 1.1.2)

Deconvolution of Tumour Profiles

Description

Deconvolution of mixed tumour profiles into normal and cancer for each patient, using the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires mixed tumour profiles and a set of unmatched "basis" normal profiles.

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Version

Install

install.packages('ISOpureR')

Monthly Downloads

296

Version

1.1.2

License

GPL-2

Maintainer

Paul Boutros

Last Published

May 1st, 2018

Functions in ISOpureR (1.1.2)

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
ISOpure.calculate.tac

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
ISOpure.util.repmat

Tiles matrix horizontally or vertically
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
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
ISOpure.step1.CPE

Perform first step of ISOpure purification algorithm
ISOpure.step2.PPE

Perform second step of ISOpure purification algorithm