gliomaClassifier: Gliomar classifier

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.