TCGA-GBM subtype tumor
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vicmonm5 • 0
@0afe4e44
Last seen 4 months ago
Spain

Hello

I am having problems accessing clinical data from TCGA-GBM. Specifically, I would like to obtain the tumor subtype of my subset of patients. Below is the code that TCGA support gave me but it doesn't work for me. I have no connection problems wiith other packages. I hope there is an alternative.

Thanks in advance

library(curatedTCGAData)
#gbm = curatedTCGAData("GBM", "RNASeq2GeneNorm", dry.run=FALSE, version = "2.1.1")
gbm = curatedTCGAData("GBM", "RNASeq2GeneNorm", dry.run=FALSE, version = "2.1.0")
curatedTCGAData • 304 views
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It would help if you showed your output that you receive when you say it doesn't work for you. Could you please provide the output and any Errors you receive.

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Hi @vicmonm5

Please use version 2.1.1 and read our release / patch notes.

To access the clinical data, you can do

colData(gbm)

To see the list of subtypes, use TCGAutils:

library(TCGAutils)
subtype_cols <- make.names(getSubtypeMap(gbm)[["GBM_subtype"]])[-1]
colData(gbm)[subtype_cols]

Best regards,

Marcel

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