> ############################################################
> # A. 普通R包: install.packages('caret')
> # B. bioconductor 包参考: https://bioconductor.org/install/
> #
> # BiocManager::install("TCGAbiolinks")
> # BiocManager::install("SummarizedExperiment")
> ############################################################
> # GDC: https://portal.gdc.cancer.gov/repository?facetTab=cases
> # project: TCGA-OV(卵巢浆液性囊腺癌)
> # 加载R包
> library(TCGAbiolinks)
> library(SummarizedExperiment)
> work_dir <-"D:/Rtcga/TCGA/share/lab/"
> # 设置程序参数
> tcga_project <- "TCGA-OV"
> data_category <- "DNA Methylation"
> platform <- "Illumina Human Methylation 27"
> sample_type <- "Primary solid Tumor"
> legacy <- FALSE
> # 设置工作目录（输出目录）
> setwd(work_dir)
> DataDirectory <- paste0(work_dir,"/GDC/",gsub("-","_",tcga_project))
> FileNameData <- paste0(DataDirectory, "_","methylation",".rda")
> ############################################################
> # 1. 下载TCGA甲基化数据
> ############################################################
> # 查询需要下载的甲基化数据（本次分析只下载肿瘤样本）
> query.met <- GDCquery(project = tcga_project,
+ legacy = legacy,
+ data.category = data_category,
+ platform = platform,
+ sample.type = sample_type)
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
|tissue.code |shortLetterCode |tissue.definition |
|:-----------|:---------------|:-------------------------------------------------|
|01 |TP |Primary Tumor |
|02 |TR |Recurrent Tumor |
|03 |TB |Primary Blood Derived Cancer - Peripheral Blood |
|04 |TRBM |Recurrent Blood Derived Cancer - Bone Marrow |
|05 |TAP |Additional - New Primary |
|06 |TM |Metastatic |
|07 |TAM |Additional Metastatic |
|08 |THOC |Human Tumor Original Cells |
|09 |TBM |Primary Blood Derived Cancer - Bone Marrow |
|10 |NB |Blood Derived Normal |
|11 |NT |Solid Tissue Normal |
|12 |NBC |Buccal Cell Normal |
|13 |NEBV |EBV Immortalized Normal |
|14 |NBM |Bone Marrow Normal |
|20 |CELLC |Control Analyte |
|40 |TRB |Recurrent Blood Derived Cancer - Peripheral Blood |
|50 |CELL |Cell Lines |
|60 |XP |Primary Xenograft Tissue |
|61 |XCL |Cell Line Derived Xenograft Tissue |
Error in checkBarcodeDefinition(sample.type) :
Primary solid Tumor was not found. Please select a difinition from the table above
