Question

GDCdownload Directory Problem :(

0

Entering edit mode

Emre • 0

@78f20378

Last seen 2.5 years 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 • 1.3k views

ADD COMMENT • link updated 9 months ago by Marcel Ramos 700 • written 2.6 years ago by Emre • 0

0

Entering edit mode

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

ADD REPLY • link 2.5 years ago Tiago C. Silva ▴ 270

0

Entering edit mode

FWIW, TCGAutils is not a related package.

ADD REPLY • link 2.5 years ago Marcel Ramos 700

0

Entering edit mode

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 months ago jain72744 • 0

0

Entering edit mode

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 9 months ago Marcel Ramos 700