Licensing | Citing | Introduction | Installation | Workflow for metrics calculated using CNV status calls | Data Input - Copy number file containing the CNV status calls | Data Importation - GRangesList | Metric Calculation | Metric Visualization | Metrics using the CNV status calls | Sørensen | Szymkiewicz–Simpson | Jaccard | Workflow for metrics calculated using the level of amplification/deletion | Data Input - Copy number file containing the level of amplification/deletion | Metrics using the level of amplification/deletion | Weighted Euclidean Distance-Based | Copy number profile simulating method | Supplementary information | Using parallelization | Creating your own GRangesList | Reproducible research | Acknowledgments | Session info | References
Package: CNVMetrics 1.17.0
Astrid Deschênes
CNVMetrics: Copy Number Variant Metrics
The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.
Authors:
CNVMetrics_1.17.0.tar.gz
CNVMetrics_1.17.0.zip(r-4.7)CNVMetrics_1.17.0.zip(r-4.6)CNVMetrics_1.17.0.zip(r-4.5)
CNVMetrics_1.17.0.tgz(r-4.6-any)CNVMetrics_1.17.0.tgz(r-4.5-any)
CNVMetrics_1.17.0.tar.gz(r-4.7-any)CNVMetrics_1.17.0.tar.gz(r-4.6-any)
CNVMetrics_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNVMetrics/json (API)
| # Install 'CNVMetrics' in R: |
| install.packages('CNVMetrics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/krasnitzlab/cnvmetrics/issues
Pkgdown/docs site:https://krasnitzlab.github.io
On BioConductor:CNVMetrics-1.17.0(bioc 3.24)CNVMetrics-1.16.0(bioc 3.23)
biologicalquestionsoftwarecopynumbervariationcnvcopy-number-variationmetricsr-language
Last updated from:39112e8a19. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 156 | ||
| linux-devel-x86_64 | OK | 232 | ||
| source / vignettes | OK | 215 | ||
| linux-release-x86_64 | OK | 249 | ||
| macos-release-arm64 | OK | 120 | ||
| macos-oldrel-arm64 | OK | 115 | ||
| windows-devel | OK | 154 | ||
| windows-release | OK | 152 | ||
| windows-oldrel | OK | 148 | ||
| wasm-release | OK | 129 |
Exports:calculateLog2ratioMetriccalculateOverlapMetricplotMetricprocessSim
Dependencies:BHBiocGenericsBiocParallelclicodetoolscpp11farverformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluegridExtragtableIRangeslabelinglambda.rlifecyclemagrittrpheatmapR6rBeta2009RColorBrewerrlangS4VectorsscalesSeqinfosnowviridisLite
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CNVMetrics: Copy number variant metrics | CNVMetrics-package CNVMetrics |
| Calculate metric using overlapping amplified/deleted regions | calculateLog2ratioMetric |
| Calculate metric using overlapping amplified/deleted regions | calculateOverlapMetric |
| Is an object of class 'CNVMetric' | is.CNVMetric |
| Plot metrics present in a 'CNVMetric' object | plotMetric |
| Print CNVMetric object | print.CNVMetric |
| Generate simulated samples with copy number profiles derived from a specific sample | processSim |
