TCGAbiolinks下载TCGA数据总结

最新版的TCGA是比对到hg38

基于RNAseq的测序count文件下载

query <- GDCquery(project = "TARGET-AML",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts")

FPKM-UQ下载

# Gene expression aligned against hg38
query <- GDCquery(project = "TCGA-GBM",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - FPKM-UQ",
                  barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"))

FPKM下载

query <- GDCquery(project = "TCGA-GBM",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - FPKM")

miRNA下载

query = GDCquery(project = "TCGA-COAD", 
                               data.category = "Transcriptome Profiling",
                               data.type = "miRNA Expression Quantification") 
query = GDCquery(project = "TARGET-AML",
                  data.category = "Transcriptome Profiling",
                  data.type = "miRNA Expression Quantification",
                  workflow.type = "BCGSC miRNA Profiling"

个性化下载—使用样本类型只获得原发性实体肿瘤样本和正常实体组织

# Using sample type to get only Primary solid Tumor samples and Solid Tissue Normal
query.mirna <- GDCquery(project = "TCGA-ACC", 
                        data.category = "Transcriptome Profiling", 
                        data.type = "miRNA Expression Quantification",
                        sample.type = c("Primary solid Tumor","Solid Tissue Normal"))

甲基化芯片数据下载

# All DNA methylation data for TCGA-GBM and TCGA-GBM
query.met <- GDCquery(project = c("TCGA-GBM","TCGA-LGG"),
                      legacy = TRUE,
                      data.category = "DNA methylation",
                      platform = c("Illumina Human Methylation 450", "Illumina Human Methylation 27"))

下载450甲基化芯片

query.met <- GDCquery(project = c("TCGA-GBM"),
                      legacy = TRUE,
                      data.category = "DNA methylation",
                      platform = c("Illumina Human Methylation 450"))

下载甲基化idat文件

# Searching idat file for DNA methylation
query <- GDCquery(project = "TCGA-OV",
                  data.category = "Raw microarray data",
                  data.type = "Raw intensities", 
                  experimental.strategy = "Methylation array", 
                  legacy = TRUE,
                  file.type = ".idat",
                  platform = "Illumina Human Methylation 450")