TCGA: to extract clinical data from barcode
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Marie DENIS ▴ 10
@marie-denis-5833
Last seen 12 months ago

Dear all,

I have a csv file containing protein levels for some TCGA patients. In this file I have the sample ID through barcodes such as TCGA-02-0011-01B-11-xxxx-xx .

I would like to obtain the associated clinical data.

When I am trying to extract the clinical data on the TCGA portal, it seems that I have one file by patient.

So I was wondering if it is possible with the R package TCGAbiolinks to link barcodes to clinical data and to obtain a global file with all clinical covariates in a "common" format as csv ?

Thanks fro your help.

Best, Marie.

cancer TCGAbiolinks • 297 views
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Ram ▴ 90
@ram
Last seen 16 days ago
United States

Have you looked at this vignette: https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/clinical.html ?

You can download the data and map identifiers later.

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Thanks for your answer.

Yes I tried some examples given in this vignette, but it seems that I obtain one file by patient ( as on the TCGA portal).

Thanks for your help.

Marie.

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Clinical data is per-patient. All samples and aliquots derived from a patient will share relevant clinical data.

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Thank you.

I tried this R command:

clin <- GDCquery_clinic("TCGA-GBM", type = "clinical", save.csv = TRUE)

But most of information were missing. Is it normal?

Thanks for your help. Marie.

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Which information was missing? Missing data should be expected in every clinical data dataset

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