Question: Clinical Data of GBM
2
gravatar for meeravarma.cev
2.5 years ago by
meeravarma.cev20 wrote:

I need clinical data of Glioblastoma patients from TCGA including Age at initial pathologic diagnosis, Date of death, Last follow up date, Ethnicity, Gender, Histological type, History of neoadjuvant treatment, Method of initial pathologic diagnosis, Karnofsky performance score, Performance status scale timing, Person neoplasm cancer status, Prior glioma, Race. How to download these data from TCGA portal giving patient or sample ID's? If anyone have this dataset, plz share as soon as possible.

clinical data glioblastoma • 1.3k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by meeravarma.cev20
4
gravatar for t.kuilman
2.5 years ago by
t.kuilman750
Netherlands
t.kuilman750 wrote:

You can do that in R using the TCGAbiolinks package (with which you can also download the actual gene expression data as follows) and follow the instructions from the Bioconductor webpage. My script would be as follows:

library("TCGAbiolinks")

DIRPREFIX <- "/PATH/"

## Download raw counts for indicated sets
## Example of TCGA.data.sets: c("TCGA-GBM")
for (id in TCGA.data.sets){
  clin.query <- GDCquery(project = id, data.category = "Clinical")
  json  <- tryCatch(GDCdownload(clin.query), 
                    error = function(e) {GDCdownload(clin.query, method = "client")})
  ## the following types of clinical data can be obtained (just pick whichever you need)
  clinical.drug <- GDCprepare_clinic(clin.query, clinical.info = "drug")
  clinical.admin <- GDCprepare_clinic(clin.query, clinical.info = "admin")
  clinical.radiation <- GDCprepare_clinic(clin.query, clinical.info = "radiation")
  clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient")
  clinical.stage_event <- GDCprepare_clinic(clin.query, clinical.info = "stage_event")
  clinical.new.tumor.event <- GDCprepare_clinic(clin.query, clinical.info = "new_tumor_event")
  clinical.followup <- GDCprepare_clinic(clin.query, clinical.info = "follow_up")
  clinical.index <- GDCquery_clinic(id, type = "clinical")
  clinical.biospecimen <- GDCquery_clinic(id, type = "biospecimen")
  save(WHAT_YOU_NEED, file = file.path(DIRPREFIX, paste0(id, "_clinical.Rdata")), compress = "xz")
}
ADD COMMENTlink modified 22 months ago • written 2.5 years ago by t.kuilman750

Hello Sir, I am trying to run your code in my 32 bit computer. It says, "cannot open url.....Windows_x64.zip". Does this work only for 64 bit computer? And also can you let me know whether I can save the whole clinical data in csv format?

ADD REPLYlink written 2.2 years ago by enigmargs0
0
gravatar for meeravarma.cev
2.5 years ago by
meeravarma.cev20 wrote:

Thank you sir for your reply.

ADD COMMENTlink written 2.5 years ago by meeravarma.cev20
1

Please use ADD COMMENT to reply to earlier posts, as such this thread remains logically structured and easy to follow. In addition, don't forget to up vote posts if an answer is helpful for and accept the post as final answer when it resolves your question.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by WouterDeCoster38k
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