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$results[]$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!