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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Failed in using barcode to filter the samples to download #444

Closed huatang5 closed 2 years ago

huatang5 commented 3 years ago

Hi, I have tried using barcode to filter the samples to download, but it didn't work. At last all the samples were downloaded. Is there any way to download some specific samples? The code is as follows.

maf_query <- GDCquery(project = "TCGA-LIHC", data.category = "Simple Nucleotide Variation", data.type = "Masked Somatic Mutation", workflow.type = 'VarScan2 Variant Aggregation and Masking', data.format = 'MAF', access = "open", barcode = c("TCGA-DD-AAEB-01A-11D-A40R-10", "TCGA-WX-AA46-01A-11D-A38X-10"), legacy = F) GDCdownload(maf_query,method = "client", files.per.chunk = 10) maf_res <- GDCprepare(maf_query) maf_res <- read.maf(maf_res)

tiagochst commented 2 years ago

barcode is used to filter files when each case has its own file. If I am not wrong Masked Somatic Mutation is one file per tumor type, you will need to filter manually.

I need to add a warning message for this case.