Package: r.jive 2.4
r.jive: Perform JIVE Decomposition for Multi-Source Data
Performs the Joint and Individual Variation Explained (JIVE) decomposition on a list of data sets when the data share a dimension, returning low-rank matrices that capture the joint and individual structure of the data [O'Connell, MJ and Lock, EF (2016) <doi:10.1093/bioinformatics/btw324>]. It provides two methods of rank selection when the rank is unknown, a permutation test and a Bayesian Information Criterion (BIC) selection algorithm. Also included in the package are three plotting functions for visualizing the variance attributed to each data source: a bar plot that shows the percentages of the variability attributable to joint and individual structure, a heatmap that shows the structure of the variability, and principal component plots.
Authors:
r.jive_2.4.tar.gz
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r.jive_2.4.tgz(r-4.4-any)r.jive_2.4.tgz(r-4.3-any)
r.jive_2.4.tar.gz(r-4.5-noble)r.jive_2.4.tar.gz(r-4.4-noble)
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r.jive.pdf |r.jive.html✨
r.jive/json (API)
| # Install 'r.jive' in R: |
| install.packages('r.jive', repos = c('https://oconnellmj.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:4cdcef90c7. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 18 2024 |
| R-4.5-win | OK | Sep 18 2024 |
| R-4.5-linux | OK | Sep 18 2024 |
| R-4.4-win | OK | Sep 18 2024 |
| R-4.4-mac | OK | Sep 18 2024 |
| R-4.3-win | OK | Sep 18 2024 |
| R-4.3-mac | OK | Sep 18 2024 |
Exports:bic.jivejivejive.iterjive.permjive.predictpjsumplot.jiveprint.jiveshow.imageshowHeatmapsshowPCAshowVarExplainedsummary.jiveSVDmisssvdwrapper
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Perform JIVE Decompositions for Multi-Source Data | r.jive-package r.jive |
| BRCA TCGA Dataset | clusts Data |
| JIVE Decomposition for Multi-source Data | bic.jive jive jive.iter jive.perm |
| Predict JIVE scores for new data | jive.predict |
| Calculate Number of Free Parameters for BIC Calculation | pjsum |
| Create Plots for a JIVE Object | plot.jive |
| Draw a Heatmap from a Matrix | show.image |
| Heatmaps for JIVE Decompositions | showHeatmaps |
| Principal Component Plots for JIVE Decomposition | showPCA |
| Display Variance Explained | showVarExplained |
| Simulated Dataset | SimData |
| JIVE Results for Simulated Dataset | Results |
| Summarize a JIVE Decomposition | print.jive summary.jive |
| Missing Data SVD | SVDmiss |
| Wrapper Function to Perform SVD | svdwrapper |
