ISOpureR: Deconvolution of Tumour Profiles

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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.

Author
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]
Date of publication
2016-08-22 20:33:25
Maintainer
Paul C Boutros <Paul.Boutros@oicr.on.ca>
License
GPL-2
Version
1.0.21

View on CRAN

Man pages

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...
ISOpure.model_optimize.vv.vv_loglikelihood
Compute the loglikelihood relevant to vv for step 1
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...
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...
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...
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...
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...
ISOpureS2.model_optimize.cc.cc_loglikelihood
Compute the loglikelihood relevant to the patient cancer...
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...
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...
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
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

Files in this package

ISOpureR
ISOpureR/inst
ISOpureR/inst/tests
ISOpureR/inst/tests/test_ISOpure_step2_beer.R
ISOpureR/inst/tests/test_ISOpure_step1_beer.R
ISOpureR/inst/extdata
ISOpureR/inst/extdata/Beer
ISOpureR/inst/extdata/Beer/alphapurities_full_dataset.txt
ISOpureR/inst/extdata/Beer/beer.tumordata.1000.transcripts.30.patients.RData
ISOpureR/inst/extdata/Beer/probeset_names.txt
ISOpureR/inst/extdata/Beer/beer.ISOpureS1model.1000.transcripts.30.patients.RData
ISOpureR/inst/extdata/Beer/beer.ISOpureS2model.1000.transcripts.30.patients.rounded.RData
ISOpureR/inst/extdata/Beer/beer.normaldata.1000.transcripts.RData
ISOpureR/inst/doc
ISOpureR/inst/doc/ISOpureRGuide.Rnw
ISOpureR/inst/doc/ISOpureRGuide.pdf
ISOpureR/tests
ISOpureR/tests/test.ISOpureS1.model_optimize.mm_functions.R
ISOpureR/tests/test.ISOpureS2.model_optimize.theta_functions.R
ISOpureR/tests/test.ISOpureS2.model_optimize.cc_functions.R
ISOpureR/tests/test.ISOpureS2.model_optimize.kappa_vv_functions.R
ISOpureR/tests/test.ISOpureS1.model_optimize.kappa_vv_omega_functions.R
ISOpureR/tests/test.ISOpureS1.model_optimize.theta_functions.R
ISOpureR/src
ISOpureR/src/rcppeigen_max_over_columns_or_rows.cpp
ISOpureR/src/RcppExports.cpp
ISOpureR/NAMESPACE
ISOpureR/NEWS
ISOpureR/R
ISOpureR/R/ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood.R
ISOpureR/R/ISOpureS2.model_optimize.theta.theta_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood.R
ISOpureR/R/ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.omega.omega_deriv_loglikelihood.R
ISOpureR/R/ISOpureS1.model_core.new_model.R
ISOpureR/R/ISOpureS1.model_optimize.opt_omega.R
ISOpureR/R/ISOpureS1.model_optimize.vv.vv_compute_loglikelihood.R
ISOpureR/R/ISOpureS2.model_core.new_model.R
ISOpureR/R/ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihood.R
ISOpureR/R/ISOpure.step1.CPE.R
ISOpureR/R/ISOpureS2.model_optimize.opt_theta.R
ISOpureR/R/ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.omega.omega_compute_loglikelihood.R
ISOpureR/R/ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood.R
ISOpureR/R/ISOpure.util.matlab_log.R
ISOpureR/R/ISOpure.util.matlab_greater_than.R
ISOpureR/R/ISOpureS2.model_optimize.cc.cc_loglikelihood.R
ISOpureR/R/ISOpureS2.model_core.optmodel.R
ISOpureR/R/ISOpure.model_optimize.vv.vv_deriv_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood.R
ISOpureR/R/ISOpure.model_optimize.vv.vv_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.opt_theta.R
ISOpureR/R/ISOpureS2.model_optimize.vv.vv_compute_loglikelihood.R
ISOpureR/R/RcppExports.R
ISOpureR/R/ISOpure.util.logsum.R
ISOpureR/R/ISOpureS1.model_optimize.omega.omega_loglikelihood.R
ISOpureR/R/ISOpureS2.model_core.compute_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.opt_kappa.R
ISOpureR/R/ISOpureS2.model_optimize.opt_cc.R
ISOpureR/R/ISOpureS1.model_optimize.opt_mm.R
ISOpureR/R/ISOpureS2.model_optimize.opt_kappa.R
ISOpureR/R/ISOpureS1.model_core.compute_loglikelihood.R
ISOpureR/R/ISOpure.model_optimize.cg_code.rminimize.R
ISOpureR/R/ISOpure.step2.PPE.R
ISOpureR/R/ISOpure.util.matlab_less_than.R
ISOpureR/R/ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.mm.mm_loglikelihood.R
ISOpureR/R/ISOpureS2.model_optimize.opt_vv.R
ISOpureR/R/ISOpureS1.model_core.optmodel.R
ISOpureR/R/ISOpureS2.model_optimize.kappa.kappa_loglikelihood.R
ISOpureR/R/ISOpureS1.model_optimize.opt_vv.R
ISOpureR/R/ISOpureS1.model_optimize.theta.theta_loglikelihood.R
ISOpureR/R/ISOpure.util.repmat.R
ISOpureR/R/ISOpureS1.model_optimize.kappa.kappa_loglikelihood.R
ISOpureR/vignettes
ISOpureR/vignettes/Figures
ISOpureR/vignettes/Figures/cancer-normal-comparison-heatmap.png
ISOpureR/vignettes/Figures/isopure.jpg
ISOpureR/vignettes/Figures/network-model.jpg
ISOpureR/vignettes/Figures/tumor-normal-comparison-heatmap.png
ISOpureR/vignettes/ISOpureRGuide.Rnw
ISOpureR/MD5
ISOpureR/build
ISOpureR/build/vignette.rds
ISOpureR/DESCRIPTION
ISOpureR/man
ISOpureR/man/ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd
ISOpureR/man/ISOpure.model_optimize.vv.vv_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_core.compute_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.opt_omega.Rd
ISOpureR/man/ISOpureS2.model_optimize.theta.theta_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_core.optmodel.Rd
ISOpureR/man/ISOpureS2.model_optimize.opt_cc.Rd
ISOpureR/man/ISOpure.util.logsum.Rd
ISOpureR/man/ISOpureS1.model_optimize.vv.vv_compute_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_optimize.opt_vv.Rd
ISOpureR/man/ISOpure.util.repmat.Rd
ISOpureR/man/ISOpure.step2.PPE.Rd
ISOpureR/man/ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_core.optmodel.Rd
ISOpureR/man/ISOpureS2.model_optimize.vv.vv_compute_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_optimize.opt_theta.Rd
ISOpureR/man/ISOpure.util.matlab_less_than.Rd
ISOpureR/man/ISOpure.model_optimize.cg_code.rminimize.Rd
ISOpureR/man/ISOpureS1.model_optimize.opt_kappa.Rd
ISOpureR/man/ISOpureS1.model_optimize.omega.omega_compute_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_core.new_model.Rd
ISOpureR/man/ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_optimize.opt_kappa.Rd
ISOpureR/man/ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.opt_mm.Rd
ISOpureR/man/ISOpureS2.model_optimize.cc.cc_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood.Rd
ISOpureR/man/ISOpure.util.matlab_log.Rd
ISOpureR/man/ISOpure.model_optimize.vv.vv_deriv_loglikelihood.Rd
ISOpureR/man/ISOpure.step1.CPE.Rd
ISOpureR/man/ISOpureS2.model_core.compute_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.mm.mm_loglikelihood.Rd
ISOpureR/man/ISOpure.util.matlab_greater_than.Rd
ISOpureR/man/ISOpureS1.model_optimize.theta.theta_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.omega.omega_loglikelihood.Rd
ISOpureR/man/ISOpureS1.model_optimize.opt_vv.Rd
ISOpureR/man/ISOpureS1.model_optimize.opt_theta.Rd
ISOpureR/man/ISOpureS1.model_optimize.omega.omega_deriv_loglikelihood.Rd
ISOpureR/man/ISOpureS2.model_core.new_model.Rd
ISOpureR/man/ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood.Rd