Inferring a topology using continuous value datasets | Artificial data | Matrix correlations | Statistical inference for matrix correlations | Statistical inference for partial matrix correlations | Inferring a topology of interactions between datasets | Inferring a topology using data type specific configuration matrices | Computing data type specific configuration matrices | Using the data type specific configuration matrices
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-4.7-any)iTOP_1.0.2.zip(r-4.6-any)iTOP_1.0.2.zip(r-4.5-any)
iTOP_1.0.2.tgz(r-4.6-any)iTOP_1.0.2.tgz(r-4.5-any)
iTOP_1.0.2.tar.gz(r-4.7-any)iTOP_1.0.2.tar.gz(r-4.6-any)
iTOP_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iTOP/json (API)
| # 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 from:872aca22c8. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 136 | ||
| source / vignettes | OK | 219 | ||
| linux-release | OK | 133 | ||
| macos-release | OK | 186 | ||
| macos-oldrel | OK | 174 | ||
| windows-devel | OK | 111 | ||
| windows-release | OK | 91 | ||
| windows-oldrel | OK | 117 | ||
| wasm-release | OK | 134 |
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 |