Hi,
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.
Many thanks.
•
written
by
berry •
This is dealt with and patched here, you'd need to figure out how to implement but author will probably be receptive to questions.
N.B. that your desired allelic_specific.seg.txt file is only available with legacy = FALSE, there are a few other file types you can review using:
query.cnv = GDCquery(project='TCGA-GBM',
data.category='Copy number variation',
legacy=T,
barcode = c("TCGA-12-5299"))
getResults(query.cnv)
Thank you for your reply.
My version is 2.17.1 and that doesn't accept sample.type = "Primary solid Tumor". It works with "Primary Tumor".
With your code, I'm only able to download "hg19.seg" file. However, I want to download a different type of segment data that is processed with ASCAT2 and file type is "allelic_specific.seg". I cannot figure out how to download it with TCGAbiolinks.
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Edit: See answer below to your actual question
Thank you very much, I appreciate it.