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This article mainly introduces "how to use TCGAbiolinks for survival analysis". In daily operation, I believe many people have doubts about how to use TCGAbiolinks for survival analysis. The editor consulted all kinds of data and sorted out simple and easy-to-use methods of operation. I hope it will be helpful to answer the doubts of "how to use TCGAbiolinks for survival analysis". Next, please follow the editor to study!

TCGAbiolinks not only provides data download function, but also provides a variety of downstream analysis functions. Survival analysis is one of the most classic application scenarios of TCGA data. Survival analysis can be easily realized through TCGAbiolinks.

Before the survival analysis, the clinical data of the patients should be obtained first. In the previous article, I introduced the method of downloading clinical data through GDC. There are two forms of clinical data in GDC.

XML

All clinical information of each sample is stored in XML format, and this file contains the most comprehensive clinical information.

TSV/JSON

After adding the data you need to download to GDCcart, you can choose to download clinical information in tsv or json format. The information obtained in this way is only a subset of the information in XML. The disadvantage is that it is not complete, but it is sufficient for survival analysis, and the survival information of patients in this file is updated faster than that of XML files.

These two kinds of clinical information can be downloaded as follows

1. TSV/JSON

The results are as follows

2. XML

The results are as follows

In addition, the function of downloading clinical information from GDC Legacy Archive database is provided, which is used as follows

In the survival analysis, it is more recommended to use the survival information in TSV/JSON format, which can be updated more timely. The specific usage is as follows

The results are as follows

At this point, the study on "how to use TCGAbiolinks for survival analysis" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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