Cargando…
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous...
Autores principales: | , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712338/ https://www.ncbi.nlm.nih.gov/pubmed/19420051 http://dx.doi.org/10.1093/bioinformatics/btp307 |
_version_ | 1782169485714653184 |
---|---|
author | Rueda, Oscar M. Diaz-Uriarte, Ramon |
author_facet | Rueda, Oscar M. Diaz-Uriarte, Ramon |
author_sort | Rueda, Oscar M. |
collection | PubMed |
description | Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found. Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http://cran.r-project.org/web/packages). Contact: rueda.om@gmail.com; rueda.om@gmail.com |
format | Text |
id | pubmed-2712338 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-27123382009-07-21 RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions Rueda, Oscar M. Diaz-Uriarte, Ramon Bioinformatics Applications Note Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found. Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http://cran.r-project.org/web/packages). Contact: rueda.om@gmail.com; rueda.om@gmail.com Oxford University Press 2009-08-01 2009-05-06 /pmc/articles/PMC2712338/ /pubmed/19420051 http://dx.doi.org/10.1093/bioinformatics/btp307 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Rueda, Oscar M. Diaz-Uriarte, Ramon RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions |
title | RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions |
title_full | RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions |
title_fullStr | RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions |
title_full_unstemmed | RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions |
title_short | RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions |
title_sort | rjacgh: bayesian analysis of acgh arrays for detecting copy number changes and recurrent regions |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712338/ https://www.ncbi.nlm.nih.gov/pubmed/19420051 http://dx.doi.org/10.1093/bioinformatics/btp307 |
work_keys_str_mv | AT ruedaoscarm rjacghbayesiananalysisofacgharraysfordetectingcopynumberchangesandrecurrentregions AT diazuriarteramon rjacghbayesiananalysisofacgharraysfordetectingcopynumberchangesandrecurrentregions |