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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.

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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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My version is 2.17.1 and that doesn't accept sample.type = "Primary solid Tumor". It works with "Primary Tumor".

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Just look into the help page of the function GDCquery!