# 项目ID,如"TCGA-BLCA" data.category, # 要下载什么数据,"Clinical"为临床,"Transcriptome Profiling"为转录组数据 data.type, # 临床信息"Clinical Supplement",表达矩阵"Gene Expression Quantification" workflow.type, # 新版的workflow.type
一、数据下载 以结肠癌数据(TCGA-COAD)为例,为了用TCGA结直肠癌数据做分析,我们首先要先整理出该癌症的基因表达矩阵(gene expression quantification数据)。(也有一些数据库提供整理好的TCGA癌症数据,如UCSC xena数据库对TCGA数据进行了整理,可直接下载表达矩阵和临床数据用于研究) 进入GDC data portal-->Respository栏...
点击logo下方的Projects，从左侧勾选框中找到Program，勾选TCGA，右侧找到需要的癌种BLCA，点击TCGA-BLCA超链接。关键步骤：精准下载指定项目数据 在弹出的对话框左上角处，点击Save New Cohort，输入名字，点击Save，关闭窗口。在左上角的下拉框选择刚刚保存好的project。步骤4：勾选下载数据 点击Repository...
[49] "TARGET-WT" "MMRF-COMMPASS" "TCGA-BLCA" [52] "NCICCR-DLBCL" "TARGET-ALL-P1" 2.data.category 可以使用TCGAbiolinks:::getProjectSummary(project)查看project中有哪些数据类型,如查询"TCGA-ACC",有7种数据类型,case_count为病人数,file_count为对应的文件数。下载表达谱,可以设置data.category="...
可以使用TCGAbiolinks:::getProjectSummary(project)查看project中有哪些数据类型,如查询"TCGA-LIHC",有7种数据类型(就是前面群主视频多次提到的数据类型),case_count为病人数,file_count为对应的文件数。小编要下载表达谱,所以设置data.category="Transcriptome Profiling" ...
>TCGAbiolinks:::getGDCprojects()$project_id[1]"TCGA-READ""TARGET-CCSK""TCGA-MESO""TCGA-CHOL"[5]"NCICCR-DLBCL""TARGET-WT""TCGA-TGCT""TCGA-PRAD"[9]"TCGA-LAML""TCGA-ESCA""TCGA-SARC""TCGA-ACC"[13]"TCGA-PAAD""TCGA-BLCA""TCGA-KICH""FM-AD"[17]"TCGA-LUSC""TCGA-THYM""TCGA-GBM"...
如需获取TCGA癌症数据, 可以使用正则表达式获取开头带有TCGA的项目. 代码语言:text AI代码解释 projects <- TCGAbiolinks::getGDCprojects()$project_id ## 获取癌症名字 projects <- projects[grepl("^TCGA", projects, perl = TRUE)] projects # [1] "TCGA-CHOL" "TCGA-LIHC" "TCGA-DLBC" "TCGA-BLCA" ...
titlePanel("TCGA下载地址获取工具"), sidebarPanel( selectInput("variable","请选择一种癌症:", list("Acute Myeloid Leukemia"="LAML", "Adrenocortical Cancer"="ACC", "Bile Duct Cancer"="CHOL", "Bladder Cancer"="BLCA", "Breast Cancer"="BRCA", ...
filename_BLCA_CNA <- DownloadCNAData(cancerType = "BLCA", assayPlatform = NULL,saveFolderName = "./BLCA/ManualExampleData/RawData.TCGA-Assembler") # 获取6例乳腺浸润性癌(BRCA)患者样本的拷贝数数据. filename_BRCA_CNA <- DownloadCNAData(cancerType = "BRCA", assayPlatform = "cna_cnv.hg19"...
可以看到,就是表达量文件稍微大一点而已,几分钟就下载好了。 癌症种类列表如下: GDC TCGA Acute Myeloid Leukemia (LAML) GDC TCGA Adrenocortical Cancer (ACC) GDC TCGA Bile Duct Cancer (CHOL) GDC TCGA Bladder Cancer (BLCA) GDC TCGA Breast Cancer (BRCA) GDC TCGA Cervical Cancer (CESC) GDC TCGA ...