Created
February 22, 2017 03:07
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Get MAF files aligned against hg19
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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)) |
Author
tiagochst
commented
Feb 22, 2017
indeed, the old hg19 has more KRAS mutations.
Thanks for looking into this.
Tommy
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