MethPed: an R package for the identification of pediatric brain tumor subtypes

BACKGROUND: DNA methylation profiling of pediatric brain tumors offers a new way of diagnosing and subgrouping these tumors which improves current clinical diagnostics based on histopathology. We have therefore developed the MethPed classifier, which is a multiclass random forest algorithm, based on...

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Autores principales: Ahamed, Mohammad Tanvir, Danielsson, Anna, Nemes, Szilárd, Carén, Helena
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930602/
https://www.ncbi.nlm.nih.gov/pubmed/27370569
http://dx.doi.org/10.1186/s12859-016-1144-0
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author Ahamed, Mohammad Tanvir
Danielsson, Anna
Nemes, Szilárd
Carén, Helena
author_facet Ahamed, Mohammad Tanvir
Danielsson, Anna
Nemes, Szilárd
Carén, Helena
author_sort Ahamed, Mohammad Tanvir
collection PubMed
description BACKGROUND: DNA methylation profiling of pediatric brain tumors offers a new way of diagnosing and subgrouping these tumors which improves current clinical diagnostics based on histopathology. We have therefore developed the MethPed classifier, which is a multiclass random forest algorithm, based on DNA methylation profiles from many subgroups of pediatric brain tumors. RESULTS: We developed an R package that implements the MethPed classifier, making it easily available and accessible. The package can be used for estimating the probability that an unknown sample belongs to each of nine pediatric brain tumor diagnoses/subgroups. CONCLUSIONS: The MethPed R package efficiently classifies pediatric brain tumors using the developed MethPed classifier. MethPed is available via Bioconductor: http://bioconductor.org/packages/MethPed/
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spelling pubmed-49306022016-07-06 MethPed: an R package for the identification of pediatric brain tumor subtypes Ahamed, Mohammad Tanvir Danielsson, Anna Nemes, Szilárd Carén, Helena BMC Bioinformatics Software BACKGROUND: DNA methylation profiling of pediatric brain tumors offers a new way of diagnosing and subgrouping these tumors which improves current clinical diagnostics based on histopathology. We have therefore developed the MethPed classifier, which is a multiclass random forest algorithm, based on DNA methylation profiles from many subgroups of pediatric brain tumors. RESULTS: We developed an R package that implements the MethPed classifier, making it easily available and accessible. The package can be used for estimating the probability that an unknown sample belongs to each of nine pediatric brain tumor diagnoses/subgroups. CONCLUSIONS: The MethPed R package efficiently classifies pediatric brain tumors using the developed MethPed classifier. MethPed is available via Bioconductor: http://bioconductor.org/packages/MethPed/ BioMed Central 2016-07-02 /pmc/articles/PMC4930602/ /pubmed/27370569 http://dx.doi.org/10.1186/s12859-016-1144-0 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Ahamed, Mohammad Tanvir
Danielsson, Anna
Nemes, Szilárd
Carén, Helena
MethPed: an R package for the identification of pediatric brain tumor subtypes
title MethPed: an R package for the identification of pediatric brain tumor subtypes
title_full MethPed: an R package for the identification of pediatric brain tumor subtypes
title_fullStr MethPed: an R package for the identification of pediatric brain tumor subtypes
title_full_unstemmed MethPed: an R package for the identification of pediatric brain tumor subtypes
title_short MethPed: an R package for the identification of pediatric brain tumor subtypes
title_sort methped: an r package for the identification of pediatric brain tumor subtypes
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930602/
https://www.ncbi.nlm.nih.gov/pubmed/27370569
http://dx.doi.org/10.1186/s12859-016-1144-0
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