Entering edit mode
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
These files should be moved after all of them are downloaded.
FWIW,
TCGAutils
is not a related package.