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.

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>
License: LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]
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:, r-release:, r-oldrel:
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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