TCGAbiolinks problem downloading ASCAT2 data
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2.1 years ago
berry ▴ 40

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.

tcgabiolinks tcga • 904 views
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Edit: See answer below to your actual question

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Thank you very much, I appreciate it.

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2.1 years ago
bruce.moran ▴ 910

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)
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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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Just look into the help page of the function GDCquery!

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