MethPed: A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
Version 1.4.0

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).

AuthorMohammad Tanvir Ahamed [aut, trl], Anna Danielsson [aut], Szilárd Nemes [aut, trl], Helena Carén [aut, cre, cph]
Bioconductor views Classification DNAMethylation Epigenetics
Date of publicationNone
MaintainerHelena Carén <helenacarenlab@gmail.com>
LicenseGPL-2
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MethPed")

Popular 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...
See all...

All man pages Function index File listing

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...

Functions

Files

DESCRIPTION
NAMESPACE
R
R/MethPed.R
R/MethPed_checkNA.R
R/MethPed_dataset.R
R/MethPed_plot.methped.R
R/MethPed_probeMis.R
R/MethPed_summary.methped.R
R/sysdata.rda
build
build/vignette.rds
data
data/MethPed_900probes.rda
data/MethPed_sample.rda
data/datalist
inst
inst/doc
inst/doc/MethPed-vignette.R
inst/doc/MethPed-vignette.Rmd
inst/doc/MethPed-vignette.html
man
man/MethPed.Rd
man/MethPed_900probes.Rd
man/MethPed_sample.Rd
man/checkNA.Rd
man/plot.methped.Rd
man/probeMis.Rd
man/summary.methped.Rd
vignettes
vignettes/MethPed-vignette.Rmd
MethPed documentation built on May 20, 2017, 9:26 p.m.

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