Package: iTOP 1.0.2
iTOP: Inferring the Topology of Omics Data
Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples. We based this methodology on the RV coefficient (Robert & Escoufier, 1976, <doi:10.2307/2347233>), a measure of matrix correlation, which we have extended for partial matrix correlations and binary data (Aben et al., 2018, <doi:10.1101/293993>).
Authors:
iTOP_1.0.2.tar.gz
iTOP_1.0.2.zip(r-4.5)iTOP_1.0.2.zip(r-4.4)iTOP_1.0.2.zip(r-4.3)
iTOP_1.0.2.tgz(r-4.4-any)iTOP_1.0.2.tgz(r-4.3-any)
iTOP_1.0.2.tar.gz(r-4.5-noble)iTOP_1.0.2.tar.gz(r-4.4-noble)
iTOP_1.0.2.tgz(r-4.4-emscripten)iTOP_1.0.2.tgz(r-4.3-emscripten)
iTOP.pdf |iTOP.html✨
iTOP/json (API)
NEWS
| # Install 'iTOP' in R: |
| install.packages('iTOP', repos = c('https://nanne-aben.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 6 years agofrom:872aca22c8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | OK | Nov 08 2024 |
| R-4.5-linux | OK | Nov 08 2024 |
| R-4.4-win | OK | Nov 08 2024 |
| R-4.4-mac | OK | Nov 08 2024 |
| R-4.3-win | OK | Nov 08 2024 |
| R-4.3-mac | OK | Nov 08 2024 |
Exports:compute.config.matricescompute.config.matrixinner.productintersect.samplesjaccardprocess.custom.config.matrixrun.bootstrapsrun.permutationsrv.coefrv.conf.intervalrv.cor.matrixrv.link.significancerv.pcorrv.pval
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Performing a single bootstrap | bootstrap.config.matrices |
| Compute configuration matrices | compute.config.matrices |
| Computes a configuration matrix | compute.config.matrix |
| Inner product similarity. | inner.product |
| Intersect samples between datasets. | intersect.samples |
| Jaccard similarity. | jaccard |
| Performing a permutation | permute.config.matrices |
| Process a custom configuration matrix. | process.custom.config.matrix |
| Bootstrapping procedure | run.bootstraps |
| Permutations for significance testing | run.permutations |
| Computes the RV coefficient | rv.coef |
| Determining a confidence interval for the (partial) RV coefficient | rv.conf.interval |
| A correlation matrix of RV coefficients | rv.cor.matrix |
| Wrapper function to determine significance in the PC algorithm | rv.link.significance |
| Determining a (partial) RV coefficient | rv.pcor |
| Determining a p-value the (partial) RV coefficient | rv.pval |
