Forest plot of MR results

Overview

This repo provides a script to reproduce a forest plot of Mendelian randomization results in Supplementary Fig. 7 (Kanai, M. et al., Nat. Genet. 2018).

Requirements

• R with metafor package.
  • To install these packages, type install.packages("metafor") in R console.

Usage

Rscript forestplot.R

Input: MR results (MR.results.txt)

This file provides the MR results from the paper. Columns correspond to the following:

• p1: Trait 1 (clinical mesurements)
• p2: Trait 2 (diseases)
• estimate: Beta estimate
• stderr: Standard error
• z: Z score
• p: P-value

Output

An example output is shown below. To get the final figure, we edited a pdf output using Adobe Illustrator.

Reference

• Kanai, M., et al. Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases. Nat. Genet. (2018) doi:10.1038/s41588-018-0047-6

Contact

Masahiro Kanai (mkanai@g.harvard.edu)

http://mkanai.github.io/

Links

• JENGER (the lab website)
• The BioBank Japan Project
• RIKEN Center for Integrative Medical Sciences
• National Bioscience Database Center Human Database