TCGA Additional Information

Go to MyBinder.

For ‘Github repository name or URL’, enter https://github.com/isb-cgc/ISB-CGC-Demos, then click ‘Launch’.

The methods in this tutorial were used to generate the R scripts used to download the data.

get_field_names.R

Download a list of all field names for the mutation data, many fields are excluded in the mutation downloader script.

TCGA_clinical_info_download.R

Download clinical information for all patients included in the mutation file download.

The downloaded file will contain both sample ID and patient ID, that can be mapped together in the final mutation file to calculate patient frequency for mutations from TCGA.

get_field_names_clinical_info.R

Download a list of all field names for the corresponding clinical data, many fields are excluded in the clinical information downloader script.