Question

GDCdownload Directory Problem :(

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Emre • 0

@78f20378

Last seen 23 months 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 • 961 views

ADD COMMENT • link updated 8 weeks ago by Marcel Ramos 690 • written 24 months ago by Emre • 0

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These files should be moved after all of them are downloaded.

ADD REPLY • link 23 months ago Tiago C. Silva ▴ 270

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FWIW, TCGAutils is not a related package.

ADD REPLY • link 23 months ago Marcel Ramos 690

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Did you find a solution for this or did you manually extract all the svs files? Furthermore, how did you process the svs files and distinguish normal to tumor sample types?

ADD REPLY • link 9 weeks ago jain72744 • 0

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FWIW, you can use the GenomicDataCommons instead:

library(GenomicDataCommons)
files() |>
    filter(cases.project.project_id == "TCGA-UVM") |>
    filter(type == "slide_image") |>
    filter(data_format == "svs") |>
    filter(experimental_strategy == "Diagnostic Slide") |>
    manifest()

ADD REPLY • link 8 weeks ago Marcel Ramos 690