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.