PPMR (Probalistic polygenic two sample mendelian randomization), isan efficient R package for two sample MR analysis, accounting for thecorrelatded instruments and the horizontal pleiotropy. PPMR can providethe estimate of causal effect, the estimates of horizontal pleitropy,and the two corresponding p values.
It is easy to install the development version of PPMR package usingthe ‘devtools’ package. The typical install time on a “normal” desktopcomputer is less than one minute.
# install.packages("devtools")library(devtools)install_github("yuanzhongshang/PPMR")The main functions isPMR_individual for individual leveldata, andPMR_summary for summary data. You can find theinstructions by ‘?PMR_individual’ and ‘?PMR_summary’.
library(PPMR)
?PMR_individual
?PMR_summary
One simple example to use the package can be found athttps://github.com/yuanzhongshang/PPMR/tree/master/example
All results from all methods used in the PPMR paper can be reproducedat https://github.com/yuanzhongshang/PPMRreproduce
This R package is developed by Zhongshang Yuan and Xiang Zhou.