Package: plasma 1.1.5

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:Kevin R. Coombes [cre, aut], Kyoko Yamaguchi [aut], Salma Abdelbaky [aut]

plasma_1.1.5.tar.gz
plasma_1.1.5.zip(r-4.7)plasma_1.1.5.zip(r-4.6)plasma_1.1.5.zip(r-4.5)
plasma_1.1.5.tgz(r-4.6-any)plasma_1.1.5.tgz(r-4.5-any)
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plasma_1.1.5.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
plasma/json (API)

# 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

Datasets:

mirESCA - ESCA type data
tfESCA - ESCA type data

On CRAN:

4.98 score 16 scripts 600 downloads 24 exports 166 dependencies

Last updated from:969e77c656. Checks:8 FAIL, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	FAIL	208
source / vignettes	OK	324
linux-release-x86_64	FAIL	215
macos-release-arm64	FAIL	98
macos-oldrel-arm64	FAIL	85
windows-devel	FAIL	100
windows-release	FAIL	84
windows-oldrel	FAIL	137
wasm-release	FAIL	216

Exports:barplot combineAllWeights fitCoxModels fitSingleModel getAllWeights getCompositeWeights getFinalWeights getSizes getTop heat image interpret loadESCAdata loadLUSCdata meanModeImputer pickSignificant plasma plasmaEnv plot predict prepareMultiOmics samplingImputer stdize summary

Dependencies:abind backports base64enc beanplot BH BiocParallel bipartite boot bootstrap broom bslib cachem car carData checkmate class cli cluster coda codetools colorspace corpcor cowplot cpp11 data.table Deriv diagram digest doBy dotCall64 dplyr ellipse evaluate farver fastmap fields fontawesome forecast foreign formatR Formula fracdiff fs futile.logger futile.options future future.apply generics ggplot2 ggrepel globals glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets igraph ipred isoband jquerylib jsonlite kernlab KernSmooth knitr labeling lambda.r lars lattice lava lifecycle listenv lme4 lmtest magrittr maps MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime minqa mixOmics modelr multcomp mvtnorm network nlme nloptr nnet numDeriv oompaBase parallelly pbkrtest permute pillar pkgconfig pls plsRcox plsRglm plyr polspline Polychrome prodlim progressr purrr quantreg R6 rappdirs rARPACK rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rgl risksetROC rlang rmarkdown rmeta rms rpart RSpectra rstudioapi S7 sandwich sass scales scatterplot3d shape sna snow spam SparseM SQUAREM statnet.common stringi stringr SuppDists survAUC survcomp survival survivalROC TH.data tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs vegan viridisLite withr xfun yaml zoo

plasma: Partial LeAst Squares for Multiomics Analysis

Rendered fromplasma.pdf.asisusingR.rsp::asis

Last update: 2022-12-01
Started: 2022-10-25

plasma: Interpretation

Rendered frominterpret.pdf.asisusingR.rsp::asis

Last update: 2022-10-25
Started: 2022-10-25

Citation

Development and contributors

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