TCGAbiolinks

library(TCGAbiolinks)

# 获取GDC工程的各种参数，如肿瘤种类等
GDCprojects=getGDCprojects()
saveRDS(object = GDCprojects,
        file = "G:\\GDCdata\\GDCprojects.rds")

建立查询

GDCquery(
  project,
  data.category,
  data.type,
  workflow.type,
  legacy = FALSE,
  access,
  platform,
  file.type,
  barcode,
  data.format,
  experimental.strategy,
  sample.type
)

project:肿瘤种类。可用TCGAbiolinks:::getGDCprojects()$project_id 查询可填的值
data.category，用TCGAbiolinks:::getProjectSummary("TCGA-BRCA") 查询，其中TCGA-BRCA来自上次查询将结果
主要是以下其中一种:

- Biospecimen
- Clinical
- Copy Number Variation
- DNA Methylation
- Sequencing Reads
- Simple Nucleotide Variation
- Transcriptome Profiling

sample.type：样本类型，取值可以是三列中的任意一个值
下载并保存

# 下载引用内容
GDCdownload(query = query_TCGA,directory = "G:\\GDCdata")
# 提取下载内容，注意路径与下载路径一致
tcga_data <- GDCprepare(query_TCGA,directory = "G:\\GDCdata")

查询结果保存,注意，不是具体数据，是查询结果描述，约等于PDATA

data <- getResults(query)