gliomaClassifier: Gliomar classifier

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

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

Author(s)

Tiago Chedraoui Silva, Tathiane Malta, Houtan Noushmehr

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)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.