R包安装

###############2.R语言的简介及相关R包的安装#######################
##2.1 R语言软件的安装
##2.2 RStudio的使用
##2.3 Rproject管理项目
getwd()   #查看当前路径
##2.4 R包的安装说明
#安装方法一：CRAN
install.packages("ggplot2")
#安装方法二：Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("limma")

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

cran_packages <- c('tidyr',
                   'tibble',
                   'dplyr',
                   'stringr',
                   'ggplot2',
                   'ggpubr',
                   'factoextra',
                   'FactoMineR') 
Biocductor_packages <- c('GEOquery',
                         'hgu133plus2.db',
                         "KEGG.db",
                         "limma",
                         "impute",
                         "GSEABase",
                         "GSVA",
                         "clusterProfiler",
                         "org.Hs.eg.db",
                         "preprocessCore",
                         "hugene10sttranscriptcluster.db")

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

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

#前面的所有提示和报错都先不要管。主要看这里
for (pkg in c(Biocductor_packages,cran_packages)){
  require(pkg,character.only=T) 
}

#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。

BiocManager::install("KEGG.db",ask = F,update = F)
source("https://bioconductor.org/biocLite.R")
biocLite("KEGG.db")