gliomaClassifier {TCGAbiolinks} | R Documentation

## Gliomar classifier

### Description

Classify DNA methylation gliomas using data from https://doi.org/10.1016/j.cell.2015.12.028

### Usage

    gliomaClassifier(data)

### Arguments

`data` | DNA methylation matrix or Summarized Experiments with samples on columns and probes on the rows

### Value

A list of 3 data frames: 1) Sample final classification 2) Each model final classification 3) Each class probability of classification

### Examples

    ## Not run:
    query <- GDCquery(project= "TCGA-GBM",
                      data.category = "DNA methylation",
                      barcode = c("TCGA-06-0122","TCGA-14-1456"),
                      platform = "Illumina Human Methylation 27",
                      legacy = TRUE)
    GDCdownload(query)
    data.hg19 <- GDCprepare(query)
    classification <- gliomaClassifier(data.hg19)

    # Comparing reslts
    TCGAquery_subtype("GBM") %>%
    dplyr::filter(patient %in% c("TCGA-06-0122","TCGA-14-1456")) %>%
    dplyr::select("patient","Supervised.DNA.Methylation.Cluster")

    ## End(Not run)

[Package TCGAbiolinks version 2.20.1 Index]