Title



     mrmodalplot -- Density plot to investigate values of phi in mrmodal



Syntax



        mrmodalplot varname_gd varname_gdse varname_gp varname_gpse [if] [in] [, options]



    options               Description
    ----------------------------------------------------------------------------------------------
      lc(optlist)         list of line colors
      lp(optlist)         list of line patterns
      lw(optlist)         list of line widths
      nome                NOME assumption
      phi(numlist)        value/s of phi (for bandwidth), default is .25 .5 1
      reps(#)             number of bootstrap replications to obtain standard error
      seed(#)             seed for random number generator for bootstrapping to obtain standard
                            error
      weighted            weighted IV estimates
      *                   Other options passed to the twoway plot



Description



    mrmodalplot plots the density of the IV estimates used in the mrmodal estimator.



    varname_gd is a variable containing the genotype-disease (SNP-outcome) association estimates.



    varname_gdse is a variable containing the genotype-disease (SNP-outcome) association estimate
    standard errors.



    varname_gp is a variable containing the genotype-phenotype (SNP-exposure) association
    estimates.



    varname_gpse is a variable containing the genotype-phenotype (SNP-exposure) association
    estimate standard errors.



    Note that in Stata 18.0 the default legend position of a twoway plot was changed from the 6
    o'clock position to the 3 o'clock position.  In Stata 18.0 and above mrmodalplot resets the
    default back to 6 o'clock (which can be overridden with, for example, legend(pos(12))).



Examples



    Using the data provided by Do et al. (2013) recreate Bowden et (2016), Figure 4, LDL-c "All
    genetic variants" (plot in row 2, column 1).



    Setup
        . use https://raw.github.com/remlapmot/mrrobust/master/dodata, clear



    Select observations (p-value with exposure < 10^-8)
        . gen byte sel1 = (ldlcp2 < 1e-8)



    Densities with phi=.25, .5, 1 and reproducible standard error
        . mrmodalplot chdbeta chdse ldlcbeta ldlcse if sel1==1, seed(12345)



    Densities with phi=.4, .6, .8, 1 and reproducible standard error
        . mrmodalplot chdbeta chdse ldlcbeta ldlcse if sel1==1, phi(.4(.2)1) seed(12345)



    Lines in grayscale and reproducible standard error
        . mrmodalplot chdbeta chdse ldlcbeta ldlcse if sel1==1, lc(gs10 gs5 gs0) seed(12345)






References



    Bowden J, Davey Smith G, Haycock PC, Burgess S. Consistent estimation in Mendelian
        randomization with some invalid instruments using a weighted median estimator. Genetic
        Epidemiology, 2016, 40, 4, 304-314.  DOI



    Do et al. Common variants associated with plasma triglycerides and risk for coronary artery
        disease. Nature Genetics, 2013, 45, 1345-1352.  DOI



Author



INCLUDE help mrrobust-author