GDCquery, copy number variation error

[sanazmo]

Hello my R version is R 4.3 and my libraries are up to date. I have a problem with GDC query. I am trying to build a gdcquery for copy number variation, but it does not work, It seems that my R could not connect to GDC portal while it works for transcription profiling and protem. how can I fix it?

[tiagochst]

Could you post the query code please ?

[sanazmo]

my codes:

query <- GDCquery(project = "TCGA-LUAD", data.category = "Copy Number Variation", data.type = "Gene Level Copy Number ",sample.type = c("Primary Tumor", "Solid Tissue Normal"),
access="open")

[tiagochst]

Could you test the code below?

query <- GDCquery(
    project = "TCGA-LUAD",
    data.category = "Copy Number Variation",
    data.type = "Gene Level Copy Number",
    access = "open"
) 
GDCdownload(query,files.per.chunk = 20) 
data <- GDCprepare(query)

[sanazmo]

thank you, It works