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- query.maf.hg19 <- GDCquery(project = "TCGA-COAD",
- data.category = "Simple nucleotide variation",
- data.type = "Simple somatic mutation",
- access = "open",
- legacy = TRUE)
- # Check maf availables
- knitr::kable(getResults(query.maf.hg19)[,c("created_datetime","file_name")])
- query.maf.hg19 <- GDCquery(project = "TCGA-COAD",
- data.category = "Simple nucleotide variation",
- data.type = "Simple somatic mutation",
- access = "open",
- file.type = "gsc_COAD_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf",
- legacy = TRUE)
- GDCdownload(query.maf.hg19)
- coad.mutect.maf <- GDCprepare(query.maf.hg19)
- library(dplyr)
- coad.mutect.maf %>% summarise(n_distinct(Tumor_Sample_Barcode))
- coad.mutect.maf %>% filter(Hugo_Symbol == "KRAS") %>% summarise(n_distinct(Tumor_Sample_Barcode))
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