Question

TCGA: to extract clinical data from barcode

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Marie DENIS ▴ 10

@marie-denis-5833

Last seen 4.2 years 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 • 2.7k views

ADD COMMENT • link updated 4.2 years ago by Kevin Blighe ★ 4.0k • written 4.2 years ago by Marie DENIS ▴ 10

score 0 · Answer 1 · 2020-09-14

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Ram ▴ 210

@ram

Last seen 6 weeks 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.

ADD COMMENT • link 4.2 years ago Ram ▴ 210

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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.

ADD REPLY • link 4.2 years ago Marie DENIS ▴ 10

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

ADD REPLY • link 4.2 years ago Ram ▴ 210

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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.

ADD REPLY • link 4.2 years ago Marie DENIS ▴ 10

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

ADD REPLY • link 4.2 years ago Kevin Blighe ★ 4.0k