1. 孟德尔随机化R包
看一篇文章,介绍孟德尔随机化分析,里面推荐了这两个R包,安装了解一下:
Methods:Genome-wide association study (GWAS) data for autoimmune diseases and AMD were obtained from the IEU Open GWAS database and the FinnGen consortium. A series of stringent SNP filtering steps was applied to ensure the reliability of the genetic instruments. MR analyses were conducted using the TwoSampleMR and MR-PRESSO packages in R. The inverse-variance weighted (IVW) method served as the primary analysis, complemented by multiple supplementary analyses and sensitivity tests.
2. R版本为4.3.1
3. 安装TwoSampleMR
最新的版本为0.6.4(2024-06-12)。下面介绍三种安装方法:
第一种:
该包没有在CRAN中,在github中,可以通过下面命令安装。
# install.packages('devtools')
devtools::install_github("MRCIEU/TwoSampleMR")
第二种:
用remote包进行安装:
install.packages("remotes")
remotes::install_github("MRCIEU/TwoSampleMR")
第三种:
也可以直接安装:
install.packages("TwoSampleMR", repos = c("https://mrcieu.r-universe.dev", "https://cloud.r-project.org"))
如果让选择是否更新,可以选择1,全部更新。
然后就是漫长的等待,把每个依赖包都更新安装好:
安装成功,载入试试:
搞定。
4. 安装TwoSampleMR
安装代码:
devtools::install_github("rondolab/MR-PRESSO")
安装成功:
后面介绍一下这两个包的使用方法。