How to link clinical data with DE miRNA data retrieved using TCGAbiolinks
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3.4 years ago
Björn ▴ 100

Hi, I managed to get "dataDEGs" for miRNAs from TCGA-PRAD database using TCGAbiolinks. I also downloaded clinical data from the TCGA. How can I introduce a "clinical.info=radiation" factor to see radiation induced DE miRNAs ?

clinical.radiation <- GDCprepare_clinic(query, clinical.info = "radiation")
datatable(clinical.radiation, options = list(scrollX = TRUE,  keys = TRUE), rownames = FALSE)

Also, how to measure "Survival" among patients with and without radiation (for selected DE miRNAs) ?

Is it better to use "legacy" or "harmonized" data for miRNAs for above analysis. Is "harmonized" data already normalized for counts.

tcgabiolinks mirna clinical • 868 views
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