inst/doc/subtypes.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)

## ----message=FALSE, warning=FALSE, include=FALSE------------------------------
library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)

## ----message=FALSE, warning=FALSE---------------------------------------------
subtypes <- PanCancerAtlas_subtypes()
DT::datatable(subtypes,
             filter = 'top',
             options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
             rownames = FALSE)

## ---- eval = FALSE------------------------------------------------------------
#  lgg.gbm.subtype <- TCGAquery_subtype(tumor = "lgg")

## ---- eval = TRUE, echo = FALSE-----------------------------------------------
datatable(
  lgg.gbm.subtype[1:10,],
  caption = "Table with LGG molecular subtypes from TCGAquery_subtype",
  filter = 'top',
  options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
  rownames = FALSE
)

## ----sessionInfo--------------------------------------------------------------
sessionInfo()