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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.
| Version: | 0.13.0 |
| Depends: | R (≥ 3.2.1), R.utils (≥ 2.11.0), aroma.core (≥ 3.2.2) |
| Imports: | utils, MASS, R.methodsS3 (≥ 1.8.1), R.oo (≥ 1.24.0), matrixStats (≥ 0.61.0), R.filesets (≥ 2.14.0) |
| Suggests: | DNAcopy |
| Published: | 2022-03-08 |
| DOI: | 10.32614/CRAN.package.calmate |
| Author: | Maria Ortiz [aut, ctb], Ander Aramburu [ctb], Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut, ctb], Angel Rubio [aut, ctb] |
| Maintainer: | Henrik Bengtsson <henrikb at braju.com> |
| BugReports: | https://github.com/HenrikBengtsson/calmate/issues |
| License: | LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)] |
| URL: | https://github.com/HenrikBengtsson/calmate/ |
| NeedsCompilation: | no |
| Citation: | calmate citation info |
| Materials: | README NEWS |
| CRAN checks: | calmate results |
| Reference manual: | calmate.pdf |
| Package source: | calmate_0.13.0.tar.gz |
| Windows binaries: | r-devel: calmate_0.13.0.zip, r-release: calmate_0.13.0.zip, r-oldrel: calmate_0.13.0.zip |
| macOS binaries: | r-release (arm64): calmate_0.13.0.tgz, r-oldrel (arm64): calmate_0.13.0.tgz, r-release (x86_64): calmate_0.13.0.tgz, r-oldrel (x86_64): calmate_0.13.0.tgz |
| Old sources: | calmate archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.