## ----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", # data.type = "Methylation Beta Value" # ) # GDCdownload(query) # dnam <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # assay(dnam)[1:5,1:2] ## ----eval = FALSE------------------------------------------------------------- # classification <- gliomaClassifier(dnam) ## ----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")