Package: calmate 0.13.0
calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
The CalMaTe method calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.
Authors:
calmate_0.13.0.tar.gz
calmate_0.13.0.zip(r-4.5)calmate_0.13.0.zip(r-4.4)calmate_0.13.0.zip(r-4.3)
calmate_0.13.0.tgz(r-4.4-any)calmate_0.13.0.tgz(r-4.3-any)
calmate_0.13.0.tar.gz(r-4.5-noble)calmate_0.13.0.tar.gz(r-4.4-noble)
calmate_0.13.0.tgz(r-4.4-emscripten)calmate_0.13.0.tgz(r-4.3-emscripten)
calmate.pdf |calmate.html✨
calmate/json (API)
NEWS
| # Install 'calmate' in R: |
| install.packages('calmate', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/henrikbengtsson/calmate/issues
acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics
Last updated 3 years agofrom:e1ce582ed1 (on master). Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 22 2024 |
| R-4.5-win | OK | Dec 22 2024 |
| R-4.5-linux | OK | Dec 22 2024 |
| R-4.4-win | OK | Dec 22 2024 |
| R-4.4-mac | OK | Dec 22 2024 |
| R-4.3-win | OK | Dec 22 2024 |
| R-4.3-mac | OK | Dec 22 2024 |
Exports:allocateOutputDataSetsallocateOutputDataSets.CalMaTeCalibrationas.character.CalMaTeCalibrationcalmatecalmateByThetaABcalmateByThetaAB.arraycalmateByTotalAndFracBcalmateByTotalAndFracB.arrayCalMaTeCalibrationfindUnitsTodo.CalMaTeCalibrationfitCalMaTefitCalMaTe.matrixfitCalMaTeCNprobesfitCalMaTeCNprobes.matrixfitCalMaTeMediansfitCalMaTeV1fitCalMaTeV2getAsteriskTags.CalMaTeCalibrationgetDataSetsgetDataSets.CalMaTeCalibrationgetFullName.CalMaTeCalibrationgetName.CalMaTeCalibrationgetOutputDataSetsgetOutputDataSets.CalMaTeCalibrationgetParameters.CalMaTeCalibrationgetPath.CalMaTeCalibrationgetReferencesgetReferences.CalMaTeCalibrationgetRootPath.CalMaTeCalibrationgetTags.CalMaTeCalibrationnbrOfFiles.CalMaTeCalibrationprocess.CalMaTeCalibrationsetTags.CalMaTeCalibrationthetaAB2TotalAndFracBthetaAB2TotalAndFracB.arraytotalAndFracB2ThetaABtotalAndFracB2ThetaAB.arraytruncateFracBtruncateFracB.arraytruncateFracB.matrixtruncateThetaABtruncateThetaAB.arraytruncateThetaAB.matrix
Dependencies:aroma.corearoma.lightbase64encBiocManagercodetoolsdigestDNAcopyfutureglobalslistenvMASSmatrixStatsparallellyPSCBSR.cacheR.devicesR.filesetsR.methodsS3R.ooR.rspR.utilsRColorBrewer
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Package calmate | calmate-package calmate |
| Normalize allele-specific copy numbers (CA,CB) | calmateByThetaAB calmateByThetaAB.array |
| Normalize allele-specific copy numbers (total,fracB) | calmateByTotalAndFracB calmateByTotalAndFracB.array |
| The CalMaTeCalibration class | CalMaTeCalibration |
