Example Analysis of TCGA data download

This article mainly introduces the TCGA data download example analysis, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

TCGAbiolinks downloads TCGA data

There are many ways to download TCGA data, which can be roughly divided into three categories:

1. Use GDC tool to download: this is actually quite troublesome, the downloaded data has to be merged, different data consolidation methods are not the same, need a lot of code.

two。 Download the collated data from the Firehose of the Broad Research Institute, but the data is relatively old.

3. Use R package to download: at present, some R packages can encapsulate GDC tools and API, simplify the operation process, and when GDC is upgraded, R package will be updated in time, so this way to download data is an ideal way.

# load the required package library (SummarizedExperiment) library (TCGAbiolinks) # GDC: https://portal.gdc.cancer.gov/############################## # # setting Environment Parameter work_dir