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.

Install the latest version of this package by entering the following in R:
install.packages("ISOpureR")
AuthorGerald 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 publication2016-08-22 20:33:25
MaintainerPaul C Boutros <Paul.Boutros@oicr.on.ca>
LicenseGPL-2
Version1.0.21

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

Functions

ISOpure.model_optimize.cg_code.rminimize Man page
ISOpure.model_optimize.vv.vv_deriv_loglikelihood Man page
ISOpure.model_optimize.vv.vv_loglikelihood Man page
ISOpureS1.model_core.compute_loglikelihood Man page
ISOpureS1.model_core.new_model Man page
ISOpureS1.model_core.optmodel Man page
ISOpureS1.model_optimize.kappa.kappa_compute_loglikelihood Man page
ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood Man page
ISOpureS1.model_optimize.kappa.kappa_loglikelihood Man page
ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood Man page
ISOpureS1.model_optimize.mm.mm_loglikelihood Man page
ISOpureS1.model_optimize.omega.omega_compute_loglikelihood Man page
ISOpureS1.model_optimize.omega.omega_deriv_loglikelihood Man page
ISOpureS1.model_optimize.omega.omega_loglikelihood Man page
ISOpureS1.model_optimize.opt_kappa Man page
ISOpureS1.model_optimize.opt_mm Man page
ISOpureS1.model_optimize.opt_omega Man page
ISOpureS1.model_optimize.opt_theta Man page
ISOpureS1.model_optimize.opt_vv Man page
ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood Man page
ISOpureS1.model_optimize.theta.theta_loglikelihood Man page
ISOpureS1.model_optimize.vv.vv_compute_loglikelihood Man page
ISOpureS2.model_core.compute_loglikelihood Man page
ISOpureS2.model_core.new_model Man page
ISOpureS2.model_core.optmodel Man page
ISOpureS2.model_optimize.cc.cc_deriv_loglikelihood Man page
ISOpureS2.model_optimize.cc.cc_loglikelihood Man page
ISOpureS2.model_optimize.kappa.kappa_compute_loglikelihood Man page
ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood Man page
ISOpureS2.model_optimize.kappa.kappa_loglikelihood Man page
ISOpureS2.model_optimize.opt_cc Man page
ISOpureS2.model_optimize.opt_kappa Man page
ISOpureS2.model_optimize.opt_theta Man page
ISOpureS2.model_optimize.opt_vv Man page
ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood Man page
ISOpureS2.model_optimize.theta.theta_loglikelihood Man page
ISOpureS2.model_optimize.vv.vv_compute_loglikelihood Man page
ISOpure.step1.CPE Man page
ISOpure.step2.PPE Man page
ISOpure.util.logsum Man page
ISOpure.util.matlab_greater_than Man page
ISOpure.util.matlab_less_than Man page
ISOpure.util.matlab_log Man page
ISOpure.util.repmat Man page

Files

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

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