突变数据下载

TCGA hg38 总的外显子基因长度可以用38M或者35

TCGAbiolinks下载:

采用TCGAbiolinks下载存在两种方式，一种是下载基于hg38的下载

#biocLite("maftools")
require(TCGAbiolinks)
require(maftools)

#下载突变数据
LIHC_mutect2 <- GDCquery_Maf(tumor = "LIHC", pipelines = "mutect2")
# Only first 50 to make render faster
datatable(LIHC_mutect2[1:20,],
          filter = 'top',
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
          rownames = FALSE)

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下载hg19的突变数据

query.maf.hg19 <- GDCquery(project = "TCGA-CHOL", 
                           data.category = "Simple nucleotide variation", 
                           data.type = "Simple somatic mutation",
                           access = "open", 
                           file.type = "bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf",
                           legacy = TRUE)
GDCdownload(query.maf.hg19)
maf <- GDCprepare(query.maf.hg19)

# Only first 50 to make render faster
datatable(maf[1:20,],
          filter = 'top',
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
          rownames = FALSE)

UCSC XENA下载

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TCGA 官网

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