Efficient statistical inference of two-sample MR (Mendelian Randomization) analysis. It can account for the correlated instruments and the horizontal pleiotropy, and can provide the accurate estimates of both causal effect and horizontal pleiotropy effect as well as the two corresponding p-values. There are two main functions in the 'PPMR' package. One is PMR_individual() for individual level data, the other is PMR_summary() for summary data.
PPMR (Probalistic polygenic two sample mendelian randomization), is an efficient R package for two sample MR analysis, accounting for the correlatded instruments and the horizontal pleiotropy. PPMR can provide the 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 using the 'devtools' package. The typical install time on a "normal" desktop computer is less than one minute.
# install.packages("devtools")
library(devtools)
install_github("yuanzhongshang/PPMR")
The main functions is PMR_individual for individual level data, and PMR_summary for summary data. You can find the instructions by '?PMR_individual' and '?PMR_summary'.
library(PPMR)
?PMR_individual
?PMR_summary
One simple example to use the package can be found at https://github.com/yuanzhongshang/PPMR/tree/master/example
All results from all methods used in the PPMR paper can be reproduced at https://github.com/yuanzhongshang/PPMRreproduce
This R package is developed by Zhongshang Yuan and Xiang Zhou.