How to link clinical data with DE miRNA data retrieved using TCGAbiolinks
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
written by vibhamishra017 •
-
Advice needed on survival analysis using TCGA
written by CaroH •
-
Tutorial: TCGA transcriptome data to R (DESeq2)
written by Barry Digby
-
TCGA-BRCA surgery date in clinical data
written by Iam •
-
Download all cases from TCGAbiolinks
written by aksam •
-
visualizing mutational data using Maftools for reference genome hg19
written by nazaninhoseinkhan
-
How to decode patient barcode inTCGA database ?
written by Björn •
-
How to link "miRNA gene quantification" and "clinical- Patient" data retrieved from TCGA
written by Björn •
-
Why "Parse XML clinical data" in TCGAbiolinks gives error in Rstudio ?
written by Björn •
-
R: Inconsistency between data from TCGAbiolinks and GDC (does TCGAbiolinks retrieve Legacy data by …
written by fr
