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TCGA数据下载分析(1-2):RTCGA包PCA和生存分析

TCGA数据下载分析(1-2):RTCGA包PCA和生存分析

作者: Y大宽 | 来源:发表于2018-08-06 17:20 被阅读84次

    1 PCA plot:pcaTCGA

    Plots Two Main Components of Principal Component Analysis

    用法如下:
    pcaTCGA(x, group.names, title = "", return.pca = FALSE, scale = TRUE, center = TRUE, var.scale = 1, obs.scale = 1, ellipse = TRUE, circle = TRUE, var.axes = FALSE, alpha = 0.8, add.lines = TRUE, ...)

    expressionsTCGA(BRCA.rnaseq, OV.rnaseq, LIHC.rnaseq) %>%
      dplyr::rename(cohort = dataset) %>%  
      filter(substr(bcr_patient_barcode, 14, 15) == "01") -> BRCA.OV.LIHC.rnaseq.cancer
    pcaTCGA(BRCA.OV.LIHC.rnaseq.cancer, "cohort") -> pca_plot
    
    plot(pca_plot)
    
    Rplot.jpeg

    2 生存分析kmTCGA()

    • Kaplan-Meier 生存曲线评估乳腺癌和卵巢癌病人中TP53基因突变与生存关系
    library(RTCGA.mutations)
    # library(dplyr) if did not load at start
    library(survminer)
    mutationsTCGA(BRCA.mutations, OV.mutations) %>%
       filter(Hugo_Symbol == 'TP53') %>%
       filter(substr(bcr_patient_barcode, 14, 15) ==
       "01") %>% # cancer tissue
       mutate(bcr_patient_barcode =
       substr(bcr_patient_barcode, 1, 12)) ->
      BRCA_OV.mutations
    
    library(RTCGA.clinical)
    survivalTCGA(
      BRCA.clinical,
      OV.clinical,
      extract.cols = "admin.disease_code"
      ) %>%
       dplyr::rename(disease = admin.disease_code) ->
      BRCA_OV.clinical
    
    BRCA_OV.clinical %>%
       left_join(
         BRCA_OV.mutations,
         by = "bcr_patient_barcode"
         ) %>%
       mutate(TP53 =
       ifelse(!is.na(Variant_Classification), "Mut","WILDorNOINFO")) ->
      BRCA_OV.clinical_mutations
    
    BRCA_OV.clinical_mutations %>%
    select(times, patient.vital_status, disease, TP53) -> BRCA_OV.2plot
    
    kmTCGA(
      BRCA_OV.2plot,
      explanatory.names = c("TP53", "disease"),
      break.time.by = 400,
      xlim = c(0,2000),
      pval = TRUE) -> km_plot
    
    print(km_plot)
    
    Rplot01.jpeg

    更多的看这里

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