Package: priorityelasticnet 1.2.1

Eunice Carrasquinha

priorityelasticnet: Comprehensive Analysis of Multi-Omics Data Using an Offset-Based Method

Priority-ElasticNet extends the Priority-LASSO method (Klau et al. (2018) <doi:10.1186/s12859-018-2344-6>) by incorporating the ElasticNet penalty, allowing for both L1 and L2 regularization. This approach fits successive ElasticNet models for several blocks of (omics) data with different priorities, using the predicted values from each block as an offset for the subsequent block. It also offers robust options to handle block-wise missingness in multi-omics data, improving the flexibility and applicability of the model in the presence of incomplete datasets.

Authors:Laila Qadir Musib [aut], Helena Mouriño [aut], Eunice Carrasquinha [aut, cre]

priorityelasticnet_1.2.1.tar.gz
priorityelasticnet_1.2.1.tar.gz(r-4.7-any)priorityelasticnet_1.2.1.tar.gz(r-4.6-any)
priorityelasticnet_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
priorityelasticnet/json (API)

# Install 'priorityelasticnet' in R:

install.packages('priorityelasticnet', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Pen_Data - Simulated Patient Data for Binary Classification

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 2 scripts 222 downloads 4 exports 227 dependencies

Last updated from:823d121240. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	240
source / vignettes	OK	382
linux-release-x86_64	OK	236
wasm-release	OK	198

Exports:cvm_priorityelasticnet missing.control priorityelasticnet weightedThreshold

Dependencies:abind AnnotationDbi askpass backports base64enc bayestestR BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob boot broom bslib cachem car carData caret checkmate cigarillo class cli clipr clock codetools colorspace commonmark corrplot cowplot cpp11 crayon curl cvms data.table datawizard DBI dbplyr DelayedArray Deriv diagram digest doBy dplyr e1071 exactRankTests farver fastmap filelock fontawesome forcats foreach forecast formatR Formula fracdiff fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glmnet glmSparseNet globals glue gower gridExtra gridtext groupdata2 gtable hardhat hms htmltools httpuv httr httr2 insight ipred IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth labeling lambda.r later lattice lava lifecycle listenv litedown lme4 lmtest lubridate magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise mgcv microbenchmark mime minqa ModelMetrics modelr MultiAssayExperiment MuMIn mvtnorm nlme nloptr nnet numbers numDeriv openssl otel parallelly parameters pbkrtest pillar pkgconfig plotrix plyr png polynom prettyunits pROC prodlim progress progressr promises proxy PRROC purrr quantreg R6 RaggedExperiment rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr rearrr recipes reformulas reshape2 restfulr Rhtslib rjson rlang rpart Rsamtools RSQLite rstatix rtracklayer rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo shape shiny snow sourcetools SparseArray SparseM sparsevctrs SQUAREM stringi stringr SummarizedExperiment survival survminer sys TCGAutils tibble tidyr tidyselect timechange timeDate tzdb UCSC.utils urca utf8 vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml zoo

Comprehensive Analysis of Multi-Omics Data Using elastic net based on priorities

Rendered frompriorityelasticnet-vignettes.Rmdusingknitr::rmarkdown

Last update: 2026-02-19
Started: 2025-01-13

Help page	Topics
Extract coefficients from a priorityelasticnet object	coef.priorityelasticnet
priorityelasticnet with several block specifications	cvm_priorityelasticnet
Construct control structures for handling of missing data for 'priorityelasticnet'	missing.control
Simulated Patient Data for Binary Classification	Pen_Data
Predictions from priorityelasticnet	predict.priorityelasticnet
Priority Elastic Net for High-Dimensional Data	priorityelasticnet
A Shiny App for Model Evaluation and Weighted Threshold Optimization	weightedThreshold

Package: priorityelasticnet 1.2.1

priorityelasticnet: Comprehensive Analysis of Multi-Omics Data Using an Offset-Based Method

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)