MethPed: A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

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Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

Author
Mohammad Tanvir Ahamed [aut, trl], Anna Danielsson [aut], Szilárd Nemes [aut, trl], Helena Carén [aut, cre, cph]
Date of publication
None
Maintainer
Helena Carén <helenacarenlab@gmail.com>
License
GPL-2
Version
1.2.0

View on Bioconductor

Man pages

checkNA
Check missing valus in dataset
MethPed
MethPed: a DNA methylation classifier tool for the...
MethPed_900probes
List of 900 probes in the predictor data
MethPed_sample
Sample dataset to MethPed package.
plot.methped
Plot conditional probability of samples that belongs to...
probeMis
Missing probe names from training data compared with input...
summary.methped
Summary of conditional probability or binary classification...

Files in this package

MethPed/DESCRIPTION
MethPed/NAMESPACE
MethPed/R
MethPed/R/MethPed.R
MethPed/R/MethPed_checkNA.R
MethPed/R/MethPed_dataset.R
MethPed/R/MethPed_plot.methped.R
MethPed/R/MethPed_probeMis.R
MethPed/R/MethPed_summary.methped.R
MethPed/R/sysdata.rda
MethPed/build
MethPed/build/vignette.rds
MethPed/data
MethPed/data/MethPed_900probes.rda
MethPed/data/MethPed_sample.rda
MethPed/data/datalist
MethPed/inst
MethPed/inst/doc
MethPed/inst/doc/MethPed-vignette.R
MethPed/inst/doc/MethPed-vignette.Rmd
MethPed/inst/doc/MethPed-vignette.html
MethPed/man
MethPed/man/MethPed.Rd
MethPed/man/MethPed_900probes.Rd
MethPed/man/MethPed_sample.Rd
MethPed/man/checkNA.Rd
MethPed/man/plot.methped.Rd
MethPed/man/probeMis.Rd
MethPed/man/summary.methped.Rd
MethPed/vignettes
MethPed/vignettes/MethPed-vignette.Rmd