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Question: GDCprepare stop working for some unknown reason
0
gravatar for ansari.sarabio
10 weeks ago by
ansari.sarabio0 wrote:

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 • 86 views
ADD COMMENTlink modified 10 weeks ago by James W. MacDonald49k • written 10 weeks ago by ansari.sarabio0

Cross-posted: https://www.biostars.org/p/353742/

ADD REPLYlink written 10 weeks ago by Kevin Blighe30
Answer: GDCprepare stop working for some unknown reason
0
gravatar for James W. MacDonald
10 weeks ago by
United States
James W. MacDonald49k wrote:

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.

ADD COMMENTlink written 10 weeks ago by James W. MacDonald49k
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