Classifying gliomas samples with gliomaClassifier


Classifying glioma samples with DNA methylation array based on:

Ceccarelli, Michele, et al. “Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma.” Cell 164.3 (2016): 550-563. (https://doi.org/10.1016/j.cell.2015.12.028)

Possible classifications are:

  • Mesenchymal-like
  • Classic-like
  • G-CIMP-high
  • G-CIMP-low
  • LGm6-GBM
  • Codel

Data


The input data can be either a Summarized Experiment object of a matrix (samples as columns, probes as rows) from the following platforms:

  • HM27
  • HM450
  • EPIC array.

In this example we will retrieve two samples from TCGA and classify them expecting the same result as the paper.

Results


The classfier will return a list of 3 data frames:

  1. Sample final classification
  2. Each model final classification
  3. Each class probability of classification

Comparing results with paper


## gbm subtype information from:doi:10.1016/j.cell.2015.12.028