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Question: How to get treatment information with TCGAbiolinks?
0
gravatar for newbie
5 months ago by
newbie0
newbie0 wrote:

Hi,

i tried to get treatment information from TCGA-COAD and TCGA-READ data, but all attempts failed.

I downloaded the harmonized, FPKM, clinical and transcriptome profiling data but couldn't find any suitable information about the treatment of the cases.

When looking at the GDC homepage, under the clinical data table I found suitable treatmant items as treatment_type: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/clinical-data-harmonization, but I have no clue how I could get them!??

Here is my code:

library(TCGAbiolinks)

# Getting clinical data
#---
# XML format:
clin.queryR <- GDCquery(project="TCGA-READ", data.category="Clinical")
GDCdownload(clin.queryR, method="client")
clinicalR <- GDCprepare_clinic(clin.queryR, clinical.info="patient")


I tried all the other clinical.info options too, but I didn't find the treatment_type information. Can you please help me how I could get the treatment_type information? Thanks a lot.

ADD COMMENTlink modified 5 months ago by Dario Strbenac1.4k • written 5 months ago by newbie0
0
gravatar for Dario Strbenac
5 months ago by
Dario Strbenac1.4k
Australia
Dario Strbenac1.4k wrote:

This is explained in the software's vignette. It seems that hardly any samples have details recorded about drug treatment, so it doesn't seem possible to incorporate patient treatment into your analysis. Perhaps another relevant dataset might be available from Gene Expression Omnibus and could have better clinical annotation of samples than TCGA does.

ADD COMMENTlink written 5 months ago by Dario Strbenac1.4k
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