Package: plasma 1.1.3

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_1.1.3.tar.gz
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plasma_1.1.3.tgz(r-4.4-any)plasma_1.1.3.tgz(r-4.3-any)
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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

Datasets:

mirESCA - ESCA type data
tfESCA - ESCA type data

On CRAN:

5.07 score 13 scripts 583 downloads 24 exports 161 dependencies

Last updated 2 months agofrom:ff29702983. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 10 2024
R-4.5-win	OK	Nov 10 2024
R-4.5-linux	OK	Nov 10 2024
R-4.4-win	OK	Nov 10 2024
R-4.4-mac	OK	Nov 10 2024
R-4.3-win	OK	Aug 21 2024
R-4.3-mac	OK	Aug 22 2024

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 fansi farver fastmap fields fontawesome foreign formatR Formula fs futile.logger futile.options future future.apply generics ggplot2 ggrepel globals glue gridExtra gsignal gtable highr Hmisc htmlTable htmltools htmlwidgets igraph ipred isoband jquerylib jsonlite kernlab KernSmooth knitr labeling lambda.r lars lattice lava lifecycle listenv lme4 magrittr maps MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime minqa mixOmics modelr multcomp munsell mvtnorm network nlme nloptr nnet numDeriv oompaBase parallelly pbkrtest permute pillar pkgconfig pls plsRcox plsRglm plyr polspline Polychrome pracma prodlim progressr purrr quantreg R6 rappdirs rARPACK RColorBrewer Rcpp RcppEigen reshape2 rgl risksetROC rlang rmarkdown rmeta rms rpart RSpectra rstudioapi sandwich sass scales scatterplot3d shape sna snow spam SparseM SQUAREM statnet.common stringi stringr SuppDists survAUC survcomp survival survivalROC TH.data tibble tidyr tidyselect tinytex utf8 vctrs vegan viridis viridisLite withr xfun yaml zoo

plasma: Interpretation

Rendered frominterpret.pdf.asisusingR.rsp::asison Nov 10 2024.

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

plasma: Partial LeAst Squares for Multiomics Analysis

Rendered fromplasma.pdf.asisusingR.rsp::asison Nov 10 2024.

Last update: 2022-12-01
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