Question: How to download TCGA mutation data by TCGAbiolinks for a subset of barcode?
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gravatar for Talip Zengin
15 months ago by
Talip Zengin10
Mugla, Turkiye
Talip Zengin10 wrote:

Hi,

I tried to download maf file for a subset of patients (n=57) through their cases barcodes by using TCGAbiolinks but it downloads all samples (n=565). I tried two different codes below:

library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)
library(maftools)

maf <- GDCquery_Maf(tumor = "LUAD", pipelines = "mutect2", save.csv = TRUE) %>% read.maf

GDCquery_Maf downloads all 565 samples and there is no barcode option for this command. It should be!!!

Then I tried this one:

query_snp <- GDCquery(project = "TCGA-LUAD",
                      data.category = "Simple Nucleotide Variation",
                      data.type = "Masked Somatic Mutation",
                      workflow.type = "MuTect2 Variant Aggregation and Masking",
                      barcode = c("TCGA-50-5930-01A-11D-1753-08"))

GDCdownload(query_snp, files.per.chunk = 100)

LUAD_snp <- GDCprepare(query_snp, save = TRUE, save.filename = "LUAD_snp.rda") %>% read.maf

But this code also downloads all 565 samples. And I could not understand the reason.

How can I download and analyze "Simple Nucleotide Variation" data of a subset of patients or samples by TCGAbiolinks?

Thanks for any help.

 

tcgabiolinks • 242 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by Talip Zengin10
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