GDCprepare stop working for some unknown reason
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@ansarisarabio-17058
Last seen 2.8 years ago

Dear all,

I am working with TCGAbiolinks for a while. It was working smoothly until now. I'd like to change some setting of the script and for an unknown reason it stops working. It asked me to start over and after it can not prepare data by GDprepare function. I get this error:

Error in if (any(duplicated(query$results[[1]]$cases)) & query$data.type != : argument is of length zero

This is my script:

#GDCquery: Searching GDC data for download
##downloading and prepare
query <- TCGAbiolinks::GDCquery(project= c("TCGA-STAD"),
                                data.category = "Transcriptome Profiling",
                                data.type = "Gene Expression Quantification",
                                workflow.type = "HTSeq - Counts",
                                file.type = "htseq.counts.gz",
                                sample.type = c("Primary solid Tumor", "Metastatic" , "Solid Tissue Normal"),
                                experimental.strategy = "RNA-Seq")
query <- TCGAbiolinks::GDCdownload(query)
library("SummarizedExperiment")
data <- TCGAbiolinks::GDCprepare(query , 
                                 save = TRUE , 
                                 save.filename = "STADesxp.rda" , 
                                 directory = "GDCdata" , 
                                 summarizedExperiment = TRUE , 
                                 remove.files.prepared = FALSE)

 

I was wondering why the package can not use the already prepared data and every time it asked for to start over.

 

Thank you very much in advance!

Sara A.

tcgabiolinks gdcprepare • 711 views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States

The function you are using is intended to download and prepare the data, and then save it in an R object. If you call that function again, it will download and prepare the data, as advertised. If you want to use the file that you have prepared, you load it into your workspace and then use it.

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