Title



     mrforest -- Forest plot for MR-Egger type models



Syntax



        mrforest varname_gd varname_gdse varname_gp varname_gpse [varname_cov] [if] [in] [,
              options]



    options                 Description
    ----------------------------------------------------------------------------------------------
      astext(#)             Percentage of plot taken up by areas for text - some trial and error
                              may be required
      effect(string)        Label for statistics column; default is Estimate
      ivid(varname)         Variable to label genotypes, usually containing RSIDs
      ividlabel(string)     Label for genotypes; default is Genotypes
      ivwlabel(string)      Label for IVW model; default is IVW
      gsort(string)         how to sort the estimates, if specified must be one of; ascending,
                              descending, or unsorted; default is ascending
      level(#)              set confidence level; default is level(95)
      mreggerlabel(string)  Label for MR-Egger model; default is MR-Egger
      mrmedianlabel(string) Label for median model; default is Median
      mrmodallabel(string)  Label for modal model; default is Modal
      models(#)             number of models to show (1 IVW, 2 & MR-Egger, 3 & Median, 4 & Modal);
                              default is 2
      modelslabel(string)   Label for models; default is Summary
      modelsonly            Only show model estimates on plot
      nonote                Suppress note reporting I^2_GX
      nostats               Suppress the statistics column
      textsize(#)           Scaling factor for text on plot. I have tried to use sensible numbers
                              here but some trial and error may be required
      zcis                  Use normal distribution CI limits (for IVW and MR-Egger)



      Options passed to other commands:
      ivwopts(string)       options for IVW estimate from mregger, ivw fe
      mreggeropts(string)   options for MR-Egger estimate from mregger
      mrivestopts(string)   options for mrivests used to generate genotype specific ratio
                              estimates and SEs
      mrmedianopts(string)  options for median estimate from mrmedian
      mrmodal(string)       options for modal estimate from mrmodal
      nofe                  Remove fe option (fixed effect SE) from the IVW fit



      *                     Other options passed to the metan



Description



    mrforest plots a forest plot for MR-Egger type models.  It is really a wrapper program for a
    call to metan (Harris et al., 2008), which must be installed.



    If you do not already have metan, it can be installed by running: ssc install metan.



    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.



    varname_cov is a variable containing the covariances between the genotype-disease
    (SNP-outcome) and genotype-phenotype (SNP-exposure) associations.






Examples



    Using the data provided by Do et al. (2013) recreate Bowden et al. (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)



    Forest plot of genotype specific IV estimates and IVW and MR-Egger estimates, labelling the
    genotypes with their RSID.
        . mrforest chdbeta chdse ldlcbeta ldlcse if sel1==1, ivid(rsid)



    Having seen the first plot we can now define nicer x-axis labels.
        . mrforest chdbeta chdse ldlcbeta ldlcse if sel1==1, ivid(rsid)
            xlabel(-5,-4,-3,-2,-1,0,1,2,3,4,5)



    Removing the column of estimates from the plot, and sorting in descending order of the IV
    estimates.
        . mrforest chdbeta chdse ldlcbeta ldlcse if sel1==1, ivid(rsid) nostats gsort(descending)



    Showing all 4 models and modifying some labels.
        . mrforest chdbeta chdse ldlcbeta ldlcse if sel1==1, ivid(rsid) models(4) modelslabel(All
            genotypes)



    If you have data which require more than 2 decimal places, use metan's undocumented dp option,
    e.g. for 4 decimal places specify dp(4)
        . gen chdbeta2 = chdbeta / 100
        . gen chdse2 = chdse / 100
        . mrforest chdbeta chdse ldlcbeta ldlcse if sel1==1, ivid(rsid) dp(4)



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



    Harris RJ, Bradburn MJ, Deeks JJ, Harbord RM, Altman DG, Sterne JAC. metan: fixed- and
        random-effects meta-analysis.  Stata Journal, 2008, 8, 1, 3-28. Link



Author



INCLUDE help mrrobust-author