gliomaClassifier {TCGAbiolinks} | R Documentation |
Classify DNA methylation gliomas using data from https://doi.org/10.1016/j.cell.2015.12.028
gliomaClassifier(data)
data |
DNA methylation matrix or Summarized Experiments with samples on columns and probes on the rows |
A list of 3 data frames: 1) Sample final classification 2) Each model final classification 3) Each class probability of classification
## 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)