GDCdownload Directory Problem :(
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Emre • 0
@78f20378
Last seen 7 weeks ago
Turkey

This Script is not saved, so the downloading process is happening in my Documents but the main problem is directory. I know the directory = "GDCdata" is default but why this data doesnt download in a path like GDCdata/TCGA-UVM etc. ? Code is creating a File which is named "GDCdata" in Documents, then All of these slide images are starting to download also in Documents. Code should be placed in three backticks as shown below

library("TCGAbiolinks")

query <- GDCquery(project = "TCGA-UVM", 
                  data.category = "Biospecimen",
                  data.type = "Slide Image", 
                  data.format = "SVS",
                  experimental.strategy="Diagnostic Slide")


GDCdownload(query,method="client",directory="GDCdata",files.per.chunk = 1)

Im going to lose my mind look what happened to my Directory

enter image description here

TCGAWorkflowData TCGAbiolinks TCGAutils • 140 views
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These files should be moved after all of them are downloaded.

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FWIW, TCGAutils is not a related package.

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