Package: ISOpureR 1.1.3

ISOpureR: Deconvolution of Tumour Profiles

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.

Authors:Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D Morris [aut], Paul C Boutros [aut, cre]

ISOpureR_1.1.3.tar.gz
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ISOpureR.pdf |ISOpureR.html✨
ISOpureR/json (API)
NEWS

# Install 'ISOpureR' in R:
install.packages('ISOpureR', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.61 score 3 stars 34 scripts 214 downloads 4 mentions 45 exports 6 dependencies

Last updated 6 years agofrom:c96fdc0e9e. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-win-x86_64NOTEOct 24 2024
R-4.5-linux-x86_64NOTEOct 24 2024
R-4.4-win-x86_64NOTEOct 24 2024
R-4.4-mac-x86_64NOTEOct 24 2024
R-4.4-mac-aarch64NOTEOct 24 2024
R-4.3-win-x86_64NOTEOct 24 2024
R-4.3-mac-x86_64NOTEOct 24 2024
R-4.3-mac-aarch64NOTEOct 24 2024

Exports:ISOpure.calculate.tacISOpure.model_optimize.cg_code.rminimizeISOpure.model_optimize.vv.vv_deriv_loglikelihoodISOpure.model_optimize.vv.vv_loglikelihoodISOpure.step1.CPEISOpure.step2.PPEISOpure.util.logsumISOpure.util.matlab_greater_thanISOpure.util.matlab_less_thanISOpure.util.matlab_logISOpure.util.repmatISOpureS1.model_core.compute_loglikelihoodISOpureS1.model_core.new_modelISOpureS1.model_core.optmodelISOpureS1.model_optimize.kappa.kappa_compute_loglikelihoodISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihoodISOpureS1.model_optimize.kappa.kappa_loglikelihoodISOpureS1.model_optimize.mm.mm_deriv_loglikelihoodISOpureS1.model_optimize.mm.mm_loglikelihoodISOpureS1.model_optimize.omega.omega_compute_loglikelihoodISOpureS1.model_optimize.omega.omega_deriv_loglikelihoodISOpureS1.model_optimize.omega.omega_loglikelihoodISOpureS1.model_optimize.opt_kappaISOpureS1.model_optimize.opt_mmISOpureS1.model_optimize.opt_omegaISOpureS1.model_optimize.opt_thetaISOpureS1.model_optimize.opt_vvISOpureS1.model_optimize.theta.theta_deriv_loglikelihoodISOpureS1.model_optimize.theta.theta_loglikelihoodISOpureS1.model_optimize.vv.vv_compute_loglikelihoodISOpureS2.model_core.compute_loglikelihoodISOpureS2.model_core.new_modelISOpureS2.model_core.optmodelISOpureS2.model_optimize.cc.cc_deriv_loglikelihoodISOpureS2.model_optimize.cc.cc_loglikelihoodISOpureS2.model_optimize.kappa.kappa_compute_loglikelihoodISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihoodISOpureS2.model_optimize.kappa.kappa_loglikelihoodISOpureS2.model_optimize.opt_ccISOpureS2.model_optimize.opt_kappaISOpureS2.model_optimize.opt_thetaISOpureS2.model_optimize.opt_vvISOpureS2.model_optimize.theta.theta_deriv_loglikelihoodISOpureS2.model_optimize.theta.theta_loglikelihoodISOpureS2.model_optimize.vv.vv_compute_loglikelihood

Dependencies:formatRfutile.loggerfutile.optionslambda.rRcppRcppEigen

Guide for using ISOpureR

Rendered fromISOpureRGuide.Rnwusingknitr::knitr_notangleon Oct 24 2024.

Last update: 2018-01-10
Started: 2013-08-25

Readme and manuals

Help Manual

Help pageTopics
Perform calculation for Tumour Adjacent Cell (TAC) profilesISOpure.calculate.tac
Minimize a differentiable multivariate functionISOpure.model_optimize.cg_code.rminimize
Compute the derivative of the loglikelihood relevant to vv for step 1ISOpure.model_optimize.vv.vv_deriv_loglikelihood
Compute the loglikelihood relevant to vv for step 1ISOpure.model_optimize.vv.vv_loglikelihood
Perform first step of ISOpure purification algorithmISOpure.step1.CPE
Perform second step of ISOpure purification algorithmISOpure.step2.PPE
Log-sum-expISOpure.util.logsum
Greater than operatorISOpure.util.matlab_greater_than
Less than operatorISOpure.util.matlab_less_than
Modified logarithm functionISOpure.util.matlab_log
Tiles matrix horizontally or verticallyISOpure.util.repmat
Compute loglikelihood given all model parameters for step 1ISOpureS1.model_core.compute_loglikelihood
Initialize a model list to hold all the parametersISOpureS1.model_core.new_model
Optimizes the ISOpure parameters for step 1ISOpureS1.model_core.optmodel
Compute loglikelihood relevant to kappa for step 1ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood
Compute derivative of loglikelihood with respect to kappa for step 1ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood
Compute loglikelihood relevant to kappa for step 1ISOpureS1.model_optimize.kappa.kappa_loglikelihood
Compute the derivative of the loglikelihood relevant to mm for step 1ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood
Compute the loglikelihood relevant to mm for step 1ISOpureS1.model_optimize.mm.mm_loglikelihood
Compute loglikelihood relevant to omega for step 1ISOpureS1.model_optimize.omega.omega_compute_loglikelihood
Compute the derivative of loglikelihood relevant to omega for step 1ISOpureS1.model_optimize.omega.omega_deriv_loglikelihood
Compute the loglikelihood relevant to omega for step 1ISOpureS1.model_optimize.omega.omega_loglikelihood
Optimize kappa in step 1ISOpureS1.model_optimize.opt_kappa
Optimize the reference cancer profile, m, in step 1ISOpureS1.model_optimize.opt_mm
Optimize omega in step 1ISOpureS1.model_optimize.opt_omega
Optimize theta in step 1ISOpureS1.model_optimize.opt_theta
Optimize vv in step 1ISOpureS1.model_optimize.opt_vv
Compute the derivative of loglikelihood relevant to theta for step 1ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood
Compute the loglikelihood relevant to theta for step 1ISOpureS1.model_optimize.theta.theta_loglikelihood
Compute loglikelihood relevant to vv for step 1ISOpureS1.model_optimize.vv.vv_compute_loglikelihood
Compute loglikelihood given all model parameters for step 2ISOpureS2.model_core.compute_loglikelihood
Compute loglikelihood given all model parameters for step 2ISOpureS2.model_core.new_model
Optimizes the ISOpure parameters for step 2ISOpureS2.model_core.optmodel
Compute the derivative of loglikelihood relevant to the patient cancer profiles, cc, for step 2ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood
Compute the loglikelihood relevant to the patient cancer profiles, cc, for step 2ISOpureS2.model_optimize.cc.cc_loglikelihood
Compute loglikelihood relevant to kappa for step 2ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihood
Compute derivative of loglikelihood with respect to kappa for step 2ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood
Compute loglikelihood relevant to kappa for step 2ISOpureS2.model_optimize.kappa.kappa_loglikelihood
Optimize the tumor-specific cancer profiles in step 2ISOpureS2.model_optimize.opt_cc
Optimize kappa in step 2ISOpureS2.model_optimize.opt_kappa
Optimize theta in step 2ISOpureS2.model_optimize.opt_theta
Optimize vv in step 2ISOpureS2.model_optimize.opt_vv
Compute the derivative of loglikelihood relevant to theta for step 2ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood
Compute the loglikelihood relevant to theta for step 2ISOpureS2.model_optimize.theta.theta_loglikelihood
Compute loglikelihood relevant to vv for step 2ISOpureS2.model_optimize.vv.vv_compute_loglikelihood