Entering edit mode
fawazfebin
▴
60
@fawazfebin-14053
Last seen 3.7 years ago
Hi
I was analysing TNBC data sets usin TCGAbiolinks and got the following error while running GDCdownload command:
> GDCdownload(query = queryDown,
+ directory = DataDirectory)
Downloading data for project TCGA-BRCA
trying URL 'https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc-client_v1.3.0_Windows_x64.zip'
Content type 'application/zip' length 16576709 bytes (15.8 MB)
downloaded 15.8 MB
Error in unzip(basename(bin)) : invalid zip name argument
In addition: Warning message:
In if (grepl("^https?://", url)) { :
the condition has length > 1 and only the first element will be used
Can anyone help please? Thanks in advance .
I have this same problem using Rstudio in windows 10 and the following code:
library(TCGAbiolinks)
data <- read.table('./R/JWCI/pc/data/prad_tcga_clinical_data.tsv', sep='\t', header=TRUE)
barcode_header <- "Patient.ID"
# get the barcodes that belong to the non-null lymph findings
barcodes <- data[barcode_header][which(!is.na(data[lymph_header]), arr.ind=TRUE)]
query <- GDCquery(project="TCGA-PRAD", data.category="Raw Sequencing Data",
barcode=barcodes)
GDCdownload(query, method = "api", directory="./R/GDCdata/")
Everything works until the end of the GDCdownload function in which i get the same error as the user above:
> GDCdownload(query, method = "api", directory="./R/GDCdata/")
Downloading data for project TCGA-PRAD
trying URL 'https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc-client_v1.3.0_Windows_x64.zip'
Content type 'application/zip' length 16576709 bytes (15.8 MB)
downloaded 15.8 MB
Error in unzip(basename(bin)) : invalid zip name argument
In addition: Warning message:
In if (grepl("^https?://", url)) { :
the condition has length > 1 and only the first element will be used