TCGA-GBM subtype tumor

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vicmonm5 • 0

@0afe4e44

Last seen 9 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 • 495 views

ADD COMMENT • link updated 9 months ago by Marcel Ramos 700 • written 9 months ago by vicmonm5 • 0

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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.

ADD REPLY • link 9 months ago shepherl 4.1k

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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

ADD REPLY • link 9 months ago Marcel Ramos 700

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