library(TCGAbiolinks)
query_luad <- GDCquery(
project = "TCGA-LUAD",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
sample.type = c("Primary Tumor")
)
> o GDCquery: Searching in GDC database
> Genome of reference: hg38
> oo Accessing GDC. This might take a while...
> ooo Project: TCGA-LUAD
> oo Filtering results
> ooo By data.type
> ooo By workflow.type
> ooo By sample.type
> oo Checking data
> ooo Checking if there are duplicated cases
> ooo Checking if there are results for the query
> o Preparing output
GDCdownload(
query = query_luad,
files.per.chunk = 10,
directory = "LUAD/"
)
> Downloading data for project TCGA-LUAD
> GDCdownload will download 540 files. A total of 2.288476735 GB
> Downloading chunk 1 of 54 (10 files, size = 42.354769 MB) as Wed_Dec_17_22_11_52_2025_0.tar.gz
> Downloading: 10 MB
> Download completed
> At least one of the chunks download was not correct. We will retry
> Downloading chunk 1 of 54 (10 files, size = 42.354769 MB) as Wed_Dec_17_22_11_52_2025_0.tar.gz
> Downloading: 10 MB
> Download completed
Error in if (ret == 1) break : argument is of length zero
