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BMC Bioinformatics. 2016 Jul 2;17(1):262. doi: 10.1186/s12859-016-1144-0.

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

Author information

1
Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden.
2
Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden.
3
Swedish Hip Arthroplasty Register, Centre of Registers Västra Götaland, Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden.
4
Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden. helena.caren@gu.se.

Abstract

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/.

KEYWORDS:

450K; Astrocytoma; Classifier (classification tool); DNA methylation; Ependymoma; Glioblastoma; Medulloblastoma; MethPed; R package; Random forest

PMID:
27370569
PMCID:
PMC4930602
DOI:
10.1186/s12859-016-1144-0
[Indexed for MEDLINE]
Free PMC Article

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