## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(dpi = 300) knitr::opts_chunk$set(cache = FALSE) ## ---- echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE--------------------- library(TCGAbiolinks) ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ library(SummarizedExperiment) library(dplyr) library(DT) ## ---- eval = FALSE, message = FALSE, results = "hide"------------------------- # 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) ## ---- eval = FALSE------------------------------------------------------------ # assay(data.hg19)[1:5,1:2] ## ---- eval = FALSE------------------------------------------------------------ # classification <- gliomaClassifier(data.hg19) ## ---- eval = FALSE------------------------------------------------------------ # names(classification) # classification$final.classification # classification$model.classifications # classification$model.probabilities ## ----------------------------------------------------------------------------- TCGAquery_subtype("GBM") %>% dplyr::filter(patient %in% c("TCGA-06-0122","TCGA-14-1456")) %>% dplyr::select("patient","Supervised.DNA.Methylation.Cluster")