Package: Umpire 2.0.10

Kevin R. Coombes

Umpire: Simulating Realistic Gene Expression and Clinical Data

The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.

Authors:Kevin R. Coombes, Jiexin Zhang, Caitlin E. Coombes

Umpire_2.0.10.tar.gz
Umpire_2.0.10.tar.gz(r-4.5-noble)Umpire_2.0.10.tar.gz(r-4.4-noble)
Umpire_2.0.10.tgz(r-4.4-emscripten)Umpire_2.0.10.tgz(r-4.3-emscripten)
Umpire.pdf |Umpire.html
Umpire/json (API)

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

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/oompa

37 exports 0.00 score 87 dependencies 218 downloads

Last updated 4 years agofrom:46c5342920eda3414b38f3a1c46658db11a4c4fb

Exports:addControlalterMeanalterSDBlockHyperParametersblurCancerEngineCancerModelClinicalEngineClinicalNoiseModelcorrelcovarEngineEngineWithActivitygetDaisyTypesgetDataTypesIndependentLogNormalIndependentNormalinvGammaMultiplemakeBlockStructuremakeDataTypesMixedTypeEngineMVNncolnComponentsnHitsPerPatternNoiseModelnormalOffsetNormalVsCancerEngineNormalVsCancerModelnPatternsnPossibleHitsnrowoutcomeCoefficientsrandsummarysurvivalCoefficientsSurvivalModel

Dependencies:abindbackportsBimodalIndexbootbriobroomcallrcarcarDatacliclustercolorspacecorrplotcowplotcpp11crayondescdiffobjdigestdplyrevaluatefansifarverfsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmc2dmclustmgcvminqamunsellmvtnormnlmenloptrnnetnumDerivoompaBasepbkrtestpillarpkgbuildpkgconfigpkgloadpolynompraiseprocessxpspurrrquantregR6RColorBrewerRcppRcppEigenrematch2rlangrprojrootrstatixscalesSparseMstringistringrsurvivaltestthattibbletidyrtidyselectutf8vctrsviridisLitewaldowithr

Umpire 2.0: Clinically Realistic Simulations

Rendered fromUmpire2.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2020-08-02
Started: 2020-04-14

Umpire Primer

Rendered fromUmpire.Rnwusingutils::Sweaveon Jun 12 2024.

Last update: 2017-07-11
Started: 2017-07-11

Umpire 2.0: Simulating Associated Survival

Rendered fromsurv.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2020-06-01
Started: 2020-06-01

Readme and manuals

Help Manual

Help pageTopics
Method "addControl"addControl addControl,ANY-method addControl,CancerEngine-method addControl,CancerModel-method addControl-method
Methods "alterMean" and "alterSD"alterMean alterMean,ANY-method alterMean-method alterSD alterSD,ANY-method alterSD-method
The "BlockHyperParameters" ClassBlockHyperParameters BlockHyperParameters-class makeBlockStructure
Method "blur"blur blur,ANY-method blur-method
The "CancerEngine" ClassCancerEngine CancerEngine-class ClinicalEngine nComponents,CancerEngine-method nrow,CancerEngine-method rand,CancerEngine-method summary,CancerEngine-method
The "CancerModel" ClassCancerModel CancerModel-class ncol,CancerModel-method nHitsPerPattern nPatterns nPossibleHits nrow,CancerModel-method outcomeCoefficients rand,CancerModel-method summary,CancerModel-method survivalCoefficients
A Noise Model for Clinical DataClinicalNoiseModel
The "Engine" ClassalterMean,Engine-method alterSD,Engine-method Engine Engine-class nComponents,Engine-method nrow,Engine-method rand,Engine-method summary,Engine-method
The "EngineWithActivity" ClassEngineWithActivity EngineWithActivity-class rand,EngineWithActivity-method summary,EngineWithActivity-method
The "IndependentLogNormal" ClassalterMean,IndependentLogNormal-method alterSD,IndependentLogNormal-method IndependentLogNormal IndependentLogNormal-class nrow,IndependentLogNormal-method rand,IndependentLogNormal-method summary,IndependentLogNormal-method
The "IndependentNormal" ClassalterMean,IndependentNormal-method alterSD,IndependentNormal-method IndependentNormal IndependentNormal-class nrow,IndependentNormal-method rand,IndependentNormal-method summary,IndependentNormal-method
Discretize a Continuous Data Set to Mixed TypesgetDaisyTypes getDataTypes makeDataTypes
The "MixedTypeEngine" ClassMixedTypeEngine MixedTypeEngine-class rand,MixedTypeEngine-method summary,MixedTypeEngine-method
The "MVN" ClassalterMean,MVN-method alterSD,MVN-method correl covar MVN MVN-class nrow,MVN-method rand,MVN-method summary,MVN-method
Method "nComponents"nComponents nComponents,ANY-method nComponents-method
The "NoiseModel" Classblur,NoiseModel-method NoiseModel NoiseModel-class summary,NoiseModel-method
Simulating Cancer Versus Normal DatasetsNormalVsCancerEngine NormalVsCancerModel
Method "rand"rand rand,ANY-method rand-method
The "SurvivalModel" Classrand,SurvivalModel-method SurvivalModel SurvivalModel-class
Transform functionsinvGammaMultiple normalOffset