In MarzyUnicz/MMRFBiolinksX:

library(MMRFBiolinksX)

# This code chunk simply makes sure that all the libraries used here are installed, it will not be shown in the report (notice echo = FALSE).
packages <- c("knitr", "dplyr", "plotly","DT","TCGAbiolinks","SummarizedExperiment")
if ( length(missing_pkgs <- setdiff(packages, rownames(installed.packages()))) > 0) {
  message("Installing missing package(s): ", paste(missing_pkgs, collapse = ", "))
  install.packages(missing_pkgs)
}

library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)

Useful information

MMRF-Compass Project

.................

Clinical indexed data

In this example we will fetch clinical indexed data (same as showed in the data portal).

clinical <- MMRFquery_clinic(type = "clinical")

clinical %>% head %>% 
  DT::datatable(filter = 'top', 
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),  
          rownames = FALSE)

MarzyUnicz/MMRFBiolinksX documentation built on April 7, 2020, 1:05 p.m.