calmate-package {calmate}

Package calmate

Description

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.

Requirements

This package depends on a set of packages that are all available via CRAN. It has been tested and verified to run on all common operating systems on which R runs, including Linux, Windows and OSX.

Installation and updates

To install this package, do install.packages("calmate").

To get started

1. To process SNP and non-polymorphic signals, see calmateByTotalAndFracB(). If you are working solely with SNP signals, calmateByThetaAB() is also available, but we recommend the former.

2. For processing data in the aroma framework, see CalMaTeCalibration.

How to cite

Please cite [1] when using CalMaTe.

License

LGPL (>= 2.1).

Author(s)

Maria Ortiz [aut, ctb], Ander Aramburu [ctb], Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut, ctb], Angel Rubio [aut, ctb].

References

[1] M. Ortiz-Estevez, A. Aramburu, H. Bengtsson, P. Neuvial and A. Rubio, CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation, Bioinformatics, 2012 [PMC3381965].