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plot_rmvmr

Source: R/plot_rmvmr.R
plot_rmvmr.Rd

Generates two radial multivariable Mendelian randomization (MVMR) plots. The first plot shows shows the estimated direct effect for each exposure obtained by fitting a radial MVMR model. Each data point shows the square root weighting for each SNP on the x-axis, and product of the ratio estimate and square root weighting for each SNP on the y-axis. These values are obtained by performing a univariate radial MR analysis for each exposure using the SNPs displayed, specifically through use of the RadialMR::ivw_radial function. Only SNPs strongly associated with the corresponding exposure are used, such that their first stage F-statistic is greater than 10. The second plot applies a correction to each ratio estimate. In both plots, the distance of each observation from the corresponding regression line is proportional to the contribution of that SNP towards global heterogeneity.

Usage

plot_rmvmr(r_input, rmvmr)

Arguments

r_input

A formatted data frame using the format_rmvmr function or an object of class MRMVInput from MendelianRandomization::mr_mvinput

rmvmr

An object containing the output from the ivw_rmvmr function of class IVW_RMVMR.

Value

An object of class "RMVMR_plot" containing the following components:

p1

A radial MVMR plot without correction

p2

A radial MVMR plot with correction

References

Spiller, W., et al., Estimating and visualising multivariable Mendelian randomization analyses within a radial framework. Forthcoming.

Author

Wes Spiller; Eleanor Sanderson; Jack Bowden.

Examples

f.data <- format_rmvmr(
    BXGs = rawdat_rmvmr[,c("ldl_beta","hdl_beta","tg_beta")],
    BYG = rawdat_rmvmr$sbp_beta,
    seBXGs = rawdat_rmvmr[,c("ldl_se","hdl_se","tg_se")],
    seBYG = rawdat_rmvmr$sbp_se,
    RSID = rawdat_rmvmr$snp)
rmvmr_output <- ivw_rmvmr(f.data, FALSE)
plot_object <- plot_rmvmr(f.data, rmvmr_output)
plot_object$p1

plot_object$p2