# TCGAbiolinks (一) 获得counts矩阵

## 加载包

- 更新包：
- BiocManager::install(“BioinformaticsFMRP/TCGAbiolinksGUI.data”)
- BiocManager::install(“BioinformaticsFMRP/TCGAbiolinks”)
- packageVersion(“TCGAbiolinks”) # 2.25.0

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    library(TCGAbiolinks)
    library(plyr)
    library(SummarizedExperiment)

## 查看信息

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    # 查看癌症类型
    TCGAbiolinks:::getGDCprojects()$project_id
    # 查看对应癌症的数据类型
    TCGAbiolinks:::getProjectSummary('TCGA-PRAD') # 以前列腺癌为例

## 筛选数据

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    # 一般的前列腺癌 GDC Data Portal 是 hg38 的
    PRAD <- GDCquery(project = 'TCGA-PRAD',
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "STAR - Counts")

    # 选择病例列 ，不加cols参数则是完整结果的全部列
    PRAD_cases <- getResults(PRAD,cols=c("cases"))

    # 选择癌组织数据
    PRAD_tp  <- TCGAquery_SampleTypes(barcode = PRAD_cases, typesample = "TP")

    PRAD_D <- GDCquery(project = 'TCGA-PRAD',
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "STAR - Counts",
                      barcode = PRAD_tp)

## 获取数据

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    PRAD_D <- GDCquery(project = 'TCGA-PRAD',
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "STAR - Counts",
                      barcode = PRAD_tp)

    GDCdownload(query = PRAD_D)

    PRAD <- GDCprepare(query = PRAD_D, save = TRUE, save.filename = "PRAD.rda")

## 获取矩阵

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    counts <- PRAD@assays@data$unstranded
    colnames(counts) <- PRAD@colData$patient
    rownames(counts) <- PRAD@rowRanges$gene_name

数据库 生信
TCGAbiolinks (一) 获得counts矩阵
https://occdn.limour.top/1655.html
Author
Limour
Posted on
March 31, 2022
Licensed under
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