TCGA代码分析流程 - 0. 安装R包

1. 设置镜像

options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
options("repos" = c(CRAN="http://mirrors.tuna.tsinghua.edu.cn/CRAN/"))

2. R包分类

cran_packages <- c("tidyr",
                   "tibble",
                   "dplyr",
                   "stringr",
                   "ggplot2",
                   "ggpubr",
                   "factoextra",
                   "FactoMineR",
                   "pheatmap",
                   "survival",
                   "survminer",
                   "patchwork",
                   "ggstatsplot",
                   "ggplotify",
                   "cowplot",
                   "glmnet",
                   "ROCR",
                   "caret",
                   "randomForest",
                   "survminer",
                   "Hmisc",
                   "e1071",
                   "deconstructSigs",
                   "timeROC"
) 
Biocductor_packages <- c("KEGG.db",
                         "limma",
                         "clusterProfiler",
                         "org.Hs.eg.db",
                         "TCGAbiolinks",
                         "SummarizedExperiment",
                         "RTCGA",
                         "RTCGA.rnaseq",
                         "RTCGA.clinical",
                         "DESeq2",
                         "edgeR",
                         "ggpubr",
                         "rtracklayer",
                         "genefilter",
                         "maftools",
                         "ComplexHeatmap",
                         "BSgenome",
                         "GDCRNATools",
                         "BSgenome.Hsapiens.UCSC.hg38"
)

3. R包安装

for (pkg in cran_packages){
  if (! require(pkg,character.only=T) ) {
    install.packages(pkg,ask = F,update = F)
    require(pkg,character.only=T) 
  }
}

if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
getOption("BioC_mirror")
getOption("repos")

for (pkg in Biocductor_packages){
  if (! require(pkg,character.only=T) ) {
    BiocManager::install(pkg,ask = F,update = F)
    require(pkg,character.only=T) 
  }
}

 4. 判断是否安装成功

前面的报错都先不要管。主要看这里

for (pkg in c(Biocductor_packages,cran_packages)){
  require(pkg,character.only=T) 
}

没有error就是成功！ 哪个报错，就回去安装哪个。

如果你没有安装xx包，却提示你xx包不存在，这也正常，是因为复杂的依赖关系，缺啥补啥。

5. 本地安装tinyarray包

if(!require(tinyarray))devtools::install_local("tinyarray-master.zip",upgrade = F)