How to programmatically download TCGA methylation beta file given a sample ID

Question

[vaysburd]

I'll appreciate an example of how to download a TCGA methylation beta file from the GDC data portal (https://portal.gdc.cancer.gov/repository) given a sample ID. E.g. what should be the format for a HTTP query?

[poisonAlien]

maybe try TCGAbiolinks They have excellent documentation to get started.

[mforde84]

this is a good option as well.

Answer 1

[mforde84]

cli client: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

restful api: https://gdc.cancer.gov/developers/gdc-application-programming-interface-api