CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.

Bioinformatics
Maria Ortiz-EstevezAngel Rubio

Abstract

CalMaTe 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. The method is available on CRAN (http://cran.r-project.org/) in the open-source R package calmate, which also includes an add-on to the Aroma Project framework (http://www.aroma-project.org/).

References

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Citations

Aug 18, 2012·Algorithms for Molecular Biology : AMB·Maria Ortiz-EstevezAngel Rubio
Nov 23, 2013·PloS One·Nicolai Juul BirkbakZhigang C Wang
Oct 2, 2014·Genome Biology·Ingrid M LönnstedtTerence P Speed
May 30, 2013·The Journal of Pathology·Pierre MartinezCharles Swanton
Sep 20, 2015·Neurology·Agustí AlentornUNKNOWN POLA Network
Apr 17, 2015·Science Translational Medicine·Nicholas McGranahanCharles Swanton
Oct 6, 2017·Briefings in Bioinformatics·Ajanthah SangaralingamClaude Chelala
Jun 14, 2017·Scientific Reports·Pierre MartinezTrevor A Graham

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