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 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/

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Klinisk medicin -- Cancer och onkologi (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Clinical Medicine -- Cancer and Oncology (hsv//eng)

Keyword

DNA methylation

450K

Random forest

R package

Glioblastoma

Medulloblastoma

Ependymoma

Classifier (classification tool)

Astrocytoma

MethPed

Biochemistry & Molecular Biology

Biotechnology & Applied Microbiology

Mathematical & Computational Biology

Publication and Content Type

ref (subject category)

art (subject category)