Introduction | System requirements and installation troubleshooting | OSX | Windows | Linux | Data required for a NetRep analysis | Tutorial data | Setting up the input lists | Running the permutation procedure to test module preservation | The module preservation statistics | Choosing the right statistics | Sparse networks | Directed networks | Sparse data | Proportional data | Homogenous modules | Small network modules | Visualising network modules | Tweaking the plot appearance | Plotting the individual components | Calculating the network properties of a module | Managing memory with large datasets | Using disk.matrix with the plotting functions | Running NetRep on a cluster | Setting the number of threads | Estimating wall time | Estimating memory usage | Optimising runtime
Package: NetRep 1.2.4
NetRep: Permutation Testing Network Module Preservation Across Datasets
Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing; Ritchie et al. (2015) <doi:10.1016/j.cels.2016.06.012>.
Authors:
NetRep_1.2.4.tar.gz
NetRep_1.2.4.zip(r-4.7)NetRep_1.2.4.zip(r-4.6)NetRep_1.2.4.zip(r-4.5)
NetRep_1.2.4.tgz(r-4.6-x86_64)NetRep_1.2.4.tgz(r-4.6-arm64)NetRep_1.2.4.tgz(r-4.5-x86_64)NetRep_1.2.4.tgz(r-4.5-arm64)
NetRep_1.2.4.tar.gz(r-4.7-arm64)NetRep_1.2.4.tar.gz(r-4.7-x86_64)NetRep_1.2.4.tar.gz(r-4.6-arm64)NetRep_1.2.4.tar.gz(r-4.6-x86_64)
NetRep_1.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
NetRep/json (API)
| # Install 'NetRep' in R: |
| install.packages('NetRep', repos = c('https://sritchie73.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sritchie73/netrep/issues
Datasets:
- discovery_correlation - Example data
- discovery_data - Example data
- discovery_network - Example data
- module_labels - Example data
- test_correlation - Example data
- test_data - Example data
- test_network - Example data
Last updated from:1a62bad2ea. Checks:8 WARNING, 2 OK, 3 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | WARNING | 263 | ||
| linux-devel-x86_64 | WARNING | 258 | ||
| source / vignettes | OK | 279 | ||
| linux-release-arm64 | WARNING | 202 | ||
| linux-release-x86_64 | WARNING | 204 | ||
| macos-release-arm64 | WARNING | 124 | ||
| macos-release-x86_64 | WARNING | 263 | ||
| macos-oldrel-arm64 | FAIL | 70 | ||
| macos-oldrel-x86_64 | FAIL | 141 | ||
| windows-devel | WARNING | 250 | ||
| windows-release | WARNING | 224 | ||
| windows-oldrel | FAIL | 85 | ||
| wasm-release | OK | 189 |
Exports:as.disk.matrixas.matrixattach.disk.matrixcombineAnalysesis.disk.matrixload.bigMatrixmodulePreservationnetworkPropertiesnodeOrderpermutationTestplotContributionplotCorrelationplotDataplotDegreeplotModuleplotNetworkplotSummaryrequiredPermssampleOrderserialize.tableshow
Dependencies:abindBHcodetoolsforeachiteratorsRColorBrewerRcppRcppArmadilloRhpcBLASctlstatmod
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'disk.matrix' class | as.disk.matrix as.disk.matrix,ANY-method as.disk.matrix,disk.matrix-method as.disk.matrix,matrix-method as.matrix,disk.matrix-method attach.disk.matrix disk.matrix is.disk.matrix serialize.table show,disk.matrix-method |
| Example data | discovery_correlation discovery_data discovery_network example-data module_labels NetRep-data test_correlation test_data test_network |
| Replication and preservation of network modules across datasets | modulePreservation |
| Fast permutation procedure for testing network module replication | NetRep |
| Calculate the topological properties for a network module | networkProperties |
| Plot the topology of a network module | plotModule |
| How many permutations do I need to test at my desired significance level? | requiredPerms |
