GSMR

GSMR (Generalised Summary-data-based Mendelian Randomisation) is a statistical method that uses GWAS summary statistics to test for a putative causal association between two phenotypes (e.g., a modifiable risk factor and a disease) based on a multi-SNP model

Installation

Packages required to be pre-installed

Please install the following packages first.

# survey
install.packages('survey')

Installation of gsmr

Please run the following to install the gsmr package:

devtools::install_github("jianyanglab/gsmr")

or download the package here and install it using the following command

install.packages("~/Downloads/gsmr_1.0.6.tar.gz", type = "source", repo = NULL)

Example analysis pipeline

Here is an example of the gsmr workflow to get started:

Under construction

Improved version of GSMR (GSMR2)

We have developed a new version of GSMR, in which the HEIDI-outlier filtering algorithm is more robust to the directional pleiotropy. Please check the GSMR2 repository if you are interested.

Citation

Zhu, Z. et al. (2018) Causal associations between risk factors and common diseases inferred from GWAS summary data. [Full text]

For questions, please email us at Jian Yang (jian.yang@westlake.edu.cn)

For bugs, please raise an issue in this repository.