calmate-package: Package calmate
In HenrikBengtsson/calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
calmate-package R Documentation
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
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.
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].
HenrikBengtsson/calmate documentation built on March 21, 2022, 6:32 p.m.
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| calmate-package | R Documentation |
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
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.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].
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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