/mr-forestplot

Primary LanguageRGNU General Public License v3.0GPL-3.0

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