download data from uidd

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Provide R access to the NCI Genomic Data Commons portal.

http://bioconductor.github.io/GenomicDataCommons/

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download data from uidd #55

Closed bioinfo-dirty-jobs closed 6 years ago

bioinfo-dirty-jobs commented 6 years ago

I have another question: I have 3 UIDD and I want to download the expression data. How can do this task?

seandavi commented 6 years ago

Everything in the GDC has a UUID, so what do the UUIDs represent (in other words, how did you get the UUIDs)? If you can share the UUIDs, that might be helpful.

bioinfo-dirty-jobs commented 6 years ago

@seandavi Thanks so much for the help.. I mean I take from paper some id like this:


bcr_patient_uuid
--
34C39A6B-DB6A-47E5-B0D4-5FA990EF7EB8
AAF93A92-2F93-477D-9EA4-D18AB7D4F258
F6509C51-3BDC-45CC-81FE-5E775236305A
F94615EA-551C-4F63-AF0D-5E49C87FC66E

and I want to donwload the expression data. What can I do?

seandavi commented 6 years ago

uuids = c("34C39A6B-DB6A-47E5-B0D4-5FA990EF7EB8",
"AAF93A92-2F93-477D-9EA4-D18AB7D4F258",
"F6509C51-3BDC-45CC-81FE-5E775236305A",
"F94615EA-551C-4F63-AF0D-5E49C87FC66E")

files() %>% 
    filter( ~ cases.case_id %in% tolower(uuids) &
                        data_type == "Gene Expression Quantification" &
                        analysis.workflow_type=="HTSeq - Counts") %>% 
    ids() %>%
    gdcdata()