RadialMR directly from the GitHub repository, first make sure you have the
devtools package installed:
RadialMR package can be installed using:
To update the package just run the
remotes::install_github("WSpiller/RadialMR") command again.
We have written the
RadialMR R package to produce radial plots and to perform radial regression for inverse variance weighted and MR-Egger regression models. The package contains a total of five functions:
format_radialfunction is used to convert a data frame containing summary data into a set format for radial analyses.
ivw_radialfunction fits a radial inverse variance weighted (IVW) model using either first order, second order, or modified second order weights. It provides an effect estimate and allows for outliers to be identified using Cochran’s Q-statistic. This function now also includes iterative and exact IVW estimation, as described in: Improving the accuracy of two-sample summary data Mendelian randomization: moving beyond the NOME assumption(https://www.biorxiv.org/content/early/2018/07/02/159442).
egger_radialfunction fits a radial MR-Egger model using either first order, second order, or modified second order weights. It provides an effect estimate and allows for outliers to be identified using Rucker’s Q-statistic.
plotly_radialfunction produces interactive radial plots corresponding to the output of the
plot_radialfunction produces a radial plot corresponding to the output of the
egger_radialfunctions. The function provides a range of scaling and aesthetic options showing either an IVW estimate, MR-Egger estimate, or both estimates simultaneously.
Radial plots are produced by many existing R packages such as
Luminescence. Care will need to be taken, however, to input data from an MR-analysis appropriately into these generic platforms. For this reason we will also continue to develop our own
RadialMR package to produce radial plots and conduct radial plot regression for the MR-setting.
The paper has been published in the International Journal of Epidemiology:
Bowden, J., et al., Improving the visualization, interpretation and analysis of two-sample summary data Mendelian randomization via the Radial plot and Radial regression. International Journal of Epidemiology, 2018. 47(4): p. 1264-1278. https://doi.org/10.1093/ije/dyy101