I have a list of cancer samples that I wish to download transcriptome data for using TCGABiolinks. I use the GDCquery() function for downloading data, however my list spans multiple TCGA projects. Here is my code
query <- GDCquery(project = "", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts", barcode = acc_numbers)
I am unsure what to put in the project argument. I do not think there is an argument for the TCGA pan cancer atlas, so does anyone know what I should do here?