inst/doc/classifiers.R

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

## ----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")