MetaboanalystR离线安装历程
做过代谢组学数据分析的人应该对这个常用的在线数据分析网站不陌生了吧,研究生阶段的时候认为可以用在线版解决问题的软件就没有管,后来发现自己没有什么进步,今天主要是给大家看一看线下版MetaboanalystR在Rstudio上安装时遇到的一些小问题吧!
安装环境:
Window 7
Rstudio
R version:3.6.3
1.安装相应的依赖包
metanr_packages <- function(){
metr_pkgs <- c("impute", "pcaMethods", "globaltest", "GlobalAncova", "Rgraphviz", "preprocessCore", "genefilter", "SSPA", "sva", "limma", "KEGGgraph", "siggenes","BiocParallel", "MSnbase", "multtest","RBGL","edgeR","fgsea","devtools","crmn","httr")
list_installed <- installed.packages()
new_pkgs <- subset(metr_pkgs, !(metr_pkgs %in% list_installed[, "Package"]))
if(length(new_pkgs)!=0){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(new_pkgs)
print(c(new_pkgs, " packages added..."))
}
if((length(new_pkgs)<1)){
print("No new packages added...")
}
}
metanr_packages()
这个环节的成功与否决定后续的离线版MetaboanalystR安装失败与否,在这个环节并不是所有包都能这样安装,对于不能进行安装的,可以下载其依赖包在本地安装
2. 本地安装包
install.packages("C:/backup/文献/MetaboAnalystR_3.0.3.tar.gz", repos = NULL, type = "source", lib="C:/Self_Software/R-3.6.3/library")
3.最后查看安装的包
vignette(package="MetaboAnalystR")
browseVignettes("MetaboAnalystR")