MethPed_900probes: List of 900 probes in the predictor data

Description

List of 900 probes in the predictor (Training data for Random Forest model)

Usage

data(MethPed_900probes)

Arguments

Value

450k methylation array probe name

Format

Data frame of 900 probes.

Details

For the construction of the training probe pool (predictors), methylation data generated by the Illumina Infinium HumanMethylation 450 BeadChip arrays were downloaded from the Gene Expression Omnibus (GEO). Four hundred seventy-two cases were available, representing several brain tumor diagnoses (DIPG, glioblastoma, ETMR, medulloblastoma, ependymoma, pilocytic astrocytoma) and their further subgroups.

The data sets were merged and probes that did not appear in all data sets were filtered away. In addition, about 190,000 CpGs were removed due to SNPs, repeats and multiple mapping sites. The final data set contained 206,823 unique probes and nine tumor classes including the medulloblastoma subgroups. K–neighbor imputation was used for missing probe data.

After that, a large number of regression analyses were performed to select the 100 probes per tumor class that had the highest predictive power (AUC values). Based on the identified 900 methylation sites, the nine pediatric brain tumor types could be accurately classified using the multiclass classification algorithm MethPed.

References

[1] Anna Danielsson, Szilárd Nemes, Magnus Tisell, Birgitta Lannering, Claes Nordborg, Magnus Sabel, and Helena Carén. "MethPed: A DNA Methylation Classifier Tool for the Identification of Pediatric Brain Tumor Subtypes". Clinical Epigenetics 2015, 7:62, 2015

Examples

Run this code

#################### Loading and view sample data
data(MethPed_900probes)
head(MethPed_900probes)

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