Package: plasma 1.1.3
![](https://r-universe.dev/static/nobody.jpg)
Kevin R. Coombes
plasma: Partial LeAst Squares for Multiomic Analysis
Contains tools for supervised analyses of incomplete, overlapping multiomics datasets. Applies partial least squares in multiple steps to find models that predict survival outcomes. See Yamaguchi et al. (2023) <doi:10.1101/2023.03.10.532096>.
Authors:
plasma_1.1.3.tar.gz
plasma_1.1.3.zip(r-4.5)plasma_1.1.3.zip(r-4.4)plasma_1.1.3.zip(r-4.3)
plasma_1.1.3.tgz(r-4.4-any)plasma_1.1.3.tgz(r-4.3-any)
plasma_1.1.3.tar.gz(r-4.5-noble)plasma_1.1.3.tar.gz(r-4.4-noble)
plasma_1.1.3.tgz(r-4.4-emscripten)plasma_1.1.3.tgz(r-4.3-emscripten)
plasma.pdf |plasma.html✨
plasma/json (API)
NEWS
# Install 'plasma' in R: |
install.packages('plasma', repos = c('https://r-forge.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/oompa
Last updated 3 days agofrom:188f1924ef. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 05 2024 |
R-4.5-win | OK | Sep 05 2024 |
R-4.5-linux | OK | Sep 05 2024 |
R-4.4-win | OK | Sep 05 2024 |
R-4.4-mac | OK | Sep 05 2024 |
R-4.3-win | OK | Aug 21 2024 |
R-4.3-mac | OK | Aug 22 2024 |
Exports:barplotcombineAllWeightsfitCoxModelsfitSingleModelgetAllWeightsgetCompositeWeightsgetFinalWeightsgetSizesgetTopheatimageinterpretloadESCAdataloadLUSCdatameanModeImputerpickSignificantplasmaplasmaEnvplotpredictprepareMultiOmicssamplingImputerstdizesummary
Dependencies:abindbackportsbase64encbeanplotBHBiocParallelbipartitebootbootstrapbroombslibcachemcarcarDatacheckmateclasscliclustercodacodetoolscolorspacecorpcorcowplotcpp11data.tableDerivdiagramdigestdoBydotCall64dplyrellipseevaluatefansifarverfastmapfieldsfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggrepelglobalsgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsigraphipredisobandjquerylibjsonlitekernlabKernSmoothknitrlabelinglambda.rlarslatticelavalifecyclelistenvlme4magrittrmapsMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamixOmicsmodelrmultcompmunsellmvtnormnetworknlmenloptrnnetnumDerivoompaBaseparallellypbkrtestpermutepillarpkgconfigplsplsRcoxplsRglmplyrpolsplinePolychromeprodlimprogressrpurrrquantregR6rappdirsrARPACKRColorBrewerRcppRcppEigenreshape2risksetROCrlangrmarkdownrmetarmsrpartRSpectrarstudioapisandwichsassscalesscatterplot3dshapesnasnowspamSparseMSQUAREMstatnet.commonstringistringrSuppDistssurvAUCsurvcompsurvivalsurvivalROCTH.datatibbletidyrtidyselecttinytexutf8vctrsveganviridisviridisLitewithrxfunyamlzoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Class '"CombinedWeights"' | combineAllWeights CombinedWeights CombinedWeights-class image,CombinedWeights-method interpret stdize summary,CombinedWeights-method |
Class '"Contribution"' | Contribution Contribution-class getAllWeights getCompositeWeights getFinalWeights getTop heat heat,Contribution-method image,Contribution-method pickSignificant summary,Contribution-method [,Contribution,ANY,ANY,ANY-method |
ESCA type data | mirESCA tfESCA |
Imputation | meanModeImputer samplingImputer |
Class '"MultiOmics"' | MultiOmics MultiOmics-class plot,MultiOmics,missing-method prepareMultiOmics summary,MultiOmics-method validMultiOmics [,MultiOmics,ANY,ANY,ANY-method |
Class '"MultiplePLSCoxModels"' | fitCoxModels getSizes MultiplePLSCoxModels MultiplePLSCoxModels-class plot,MultiplePLSCoxModels,missing-method predict,MultiplePLSCoxModels-method summary,MultiplePLSCoxModels-method validMultipleCoxModels [,MultiplePLSCoxModels,ANY,ANY,ANY-method |
Class '"plasma"' | barplot,plasma-method plasma plasma-class plot,plasma,missing-method predict,plasma-method summary,plasma-method |
Class '"plasmaPredictions"' | plasmaPredictions plasmaPredictions-class plot,plasmaPredictions,missing-method |
Class '"SingleModel"' | fitSingleModel plot,SingleModel,missing-method predict,SingleModel-method SingleModel-class summary,SingleModel-method |
Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA). | assemble loadESCAdata loadLUSCdata m450info Outcome plasmaEnv TCGA-ESCA TCGA-LUSC |