Package: woven 0.99.3

Nathan Bresette

woven: Weighted Omics View Embedding via Nystrom for Incomplete Multi-Omics Data

Supervised multi-omics integration for block-missing ("ragged") data. WOVEN learns a shared latent space across V omics modalities using only fully-observed anchor subjects, then projects block-missing subjects via Nystrom extension without feature-level imputation. Supervision enters through a label-augmented cross-covariance (analogous to DIABLO), and projection matrices can optionally be ridge-regularized and univariately feature-screened for high-dimensional modalities. Designed for comparative effectiveness research where intersection-only methods introduce selection bias.

Authors:Nathan Bresette [aut, cre], Ai-Ling Lin [aut], Jianlin Cheng [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
woven/json (API)

# Install 'woven' in R:

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

Bug tracker:https://github.com/nathanbresette/woven/issues

Datasets:

woven_example - Example dataset for WOVEN

On CRAN:

software statisticalmethod multiplecomparison geneexpression transcriptomics proteomics metabolomics dimensionreduction clustering classification sequencing

3.40 score 3 scripts 23 exports 15 dependencies

Last updated from:5f9ecfb94b. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	193
linux-devel	OK	195
source / vignettes	OK	207
linux-release	OK	191
macos-release	OK	134
macos-oldrel	OK	102
windows-devel	OK	144
windows-release	OK	122
windows-oldrel	OK	145
wasm-release	OK	165

Exports:anchorIdx plot show singularValues summary WList woven woven_davies_bouldin woven_effect_bias woven_ess_retention woven_mcca_dual woven_metrics woven_nmi woven_nystrom_error woven_plot_loadings woven_plot_variance woven_plot_vip woven_precompute woven_predict woven_rv woven_scores woven_silhouette Z

Dependencies:BH BiocParallel cluster codetools cpp11 formatR futile.logger futile.options lambda.r lattice Matrix MatrixGenerics matrixStats RANN snow

Introduction to WOVEN: Multi-Omics Integration for Incomplete Patient Data

Rendered fromwoven-intro.Rmdusingknitr::rmarkdown

Last update: 2026-09-17
Started: 2026-06-16

Help page	Topics
Indices of the anchor (fully-observed) subjects	anchorIdx anchorIdx,woven-method
Plot the WOVEN latent space	plot,woven,missing-method
Show method for WOVEN fit	show,woven-method
Supervised canonical correlations	singularValues singularValues,woven-method
Summarise a WOVEN fit	summary,woven-method
Per-modality projection matrices	WList WList,woven-method
Fit a supervised WOVEN model	woven
Davies-Bouldin index	woven_davies_bouldin
CER-specific: subgroup effect estimate bias	woven_effect_bias
Effective sample size retention	woven_ess_retention
Example dataset for WOVEN	woven_example
Fit supervised WOVEN for V >= 2 views via dual SUMCOR MCCA (closed-form)	woven_mcca_dual
Convenience wrapper: compute core metrics directly from a woven fit	woven_metrics
Normalized mutual information between cluster assignments and true labels	woven_nmi
Leave-anchor-out Nystrom projection error	woven_nystrom_error
Plot feature loadings for one WOVEN latent dimension	woven_plot_loadings
Plot variance explained per WOVEN latent dimension	woven_plot_variance
Plot VIP scores for a WOVEN modality	woven_plot_vip
Pre-compute Laplacian graphs for reuse across multiple woven() calls	woven_precompute
Predict class probabilities for new subjects	woven_predict
RV coefficient between latent scores and ground-truth factor matrix	woven_rv
Extract latent scores for new subjects	woven_scores
Average silhouette width	woven_silhouette
S4 class for a fitted WOVEN model	woven-class
Consensus latent scores	Z Z,woven-method

Package: woven 0.99.3

woven: Weighted Omics View Embedding via Nystrom for Incomplete Multi-Omics Data

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