How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons

Question

[Hashirama]

Dear community,

I am totally new to TCGA and Bioconductor and I am really confused how to obtain more clinical data (e.g. for survival analysis, gender, RNA-seq read count data, ...) from some cases I got. For every "patient" I have

• gdc_file_uuid (e.g. 52F6329C-CDC6-4196-A4A0-58952332905C)
• filename (e.g. UNCID_1552290.d6b7779f-a245-48ee-b9a8-2570c023a531.sorted_genome_alignments.bam)
• case_uuid (e.g. 2be42cc2-9b97-4821-afc2-d1e42eb3932d)

How can I use this in the R package GenomicDataCommons to get more clinical data?

I would be glad for any help!

Kind regards, Hashirama

[ATpoint]

I am not familiar with that particular package, but you should be able to retrieve and TCGA-related information via the well-documented TCGAbiolinks, see https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/clinical.html

Answer 1

[ATpoint]

Answered by the package developer: https://support.bioconductor.org/p/9140873/