I want to download TCGA copy number segment data that is created by ASCAT2 using TCGAbiolinks but I can't specify this data type. Is there a way to do that? I am used to downloading with GDCquery but this time I fail.
The files I want to download end in this format "allelic_specific.seg" but I can't specify this file type unlike "nocnv_hg19.seg".
I tried the following in many ways either I get an error or the "nocnv_hg19.seg.txt" files.
cnv.query <- GDCquery(project = "TCGA-GBM", data.category = "Copy number variation", legacy = TRUE, #workflow.type = "ASCAT2", data.type = "Copy number segmentation", #file.type = "allelic_specific.seg", platform = "Affymetrix SNP Array 6.0", sample.type = "Primary Tumor", barcode = c("TCGA-12-5299"))
Hope somebody knows how to tackle this.