'Why this R code has Directory problem for GDCdownload?
The main problem is directory. I know the directory = "GDCdata" is default but why this data doesnt download in a path like Documents/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.
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",files.per.chunk = 1)
This code ruined my documents like this,
When I changed directory from default to = "Data" nothing changed, is this program downloading data like this? When I check https://rdrr.io/bioc/TCGAbiolinks/man/GDCdownload.html here. The path should be like this, example_data_dir/TARGET-AML/harmonized/Transcriptome_Profiling/miRNA_Expression_Quantification
I am going to lose my mind
Sources
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