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mrmodal.sthlp
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mrmodal.sthlp
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{smcl}
{* *! version 0.1.0 2jun2017 Tom Palmer}{...}
{vieweralsosee "mrrobust" "help mrrobust"}{...}
{viewerjumpto "Syntax" "mrmodal##syntax"}{...}
{viewerjumpto "Description" "mrmodal##description"}{...}
{viewerjumpto "Options" "mrmodal##options"}{...}
{viewerjumpto "Examples" "mrmodal##examples"}{...}
{viewerjumpto "Stored results" "mrmodal##results"}{...}
{viewerjumpto "References" "mrmodal##references"}{...}
{viewerjumpto "Author" "mrmodal##author"}{...}
{title:Title}
{p 5}
{bf:mrmodal} {hline 2} Modal estimator for summary data
{p_end}
{marker syntax}{...}
{title:Syntax}
{p 8 16 2}
{opt mrmodal} {var:_gd} {var:_gdse} {var:_gp} {var:_gpse} {ifin}
[{cmd:,} {it:options}]
{synoptset 20 tabbed}{...}
{synopthdr}
{synoptline}
{synopt :{opt l:evel(#)}}set confidence level; default is {cmd:level(95)}{p_end}
{synopt :{opt nome:}}NOME assumption{p_end}
{synopt :{opt nosave:}}Do not save density and vector of IV estimates in Mata{p_end}
{synopt :{opt phi:(#)}}value of phi (for bandwidth){p_end}
{synopt :{opt reps:(#)}}number of bootstrap replications to obtain standard error{p_end}
{synopt :{opt seed:(#)}}seed for random number generator for bootstrapping to
obtain standard error{p_end}
{synopt :{opt weight:ed}}weighted IV estimates{p_end}
{marker description}{...}
{title:Description}
{pstd}
{cmd:mrmodal} implements the zero modal estimator of {help mrmodal##hartwig:Hartwig et al. (2017)}
for use with summary level data (i.e. reported genotype-disease [SNP-outcome] and genotype-phenotype
[SNP-exposure] association estimates and their standard errors for individual genotypes).
{pstd}
Standard errors are obtained by parametric bootstrapping.
{pstd}
{var:_gd} is a variable containing the genotype-disease (SNP-outcome) association estimates.
{pstd}
{var:_gdse} is a variable containing the genotype-disease (SNP-outcome) association estimate
standard errors.
{pstd}
{var:_gp} is a variable containing the genotype-phenotype (SNP-exposure) association
estimates.
{pstd}
{var:_gpse} is a variable containing the genotype-phenotype (SNP-exposure) association
estimate standard errors.
{marker options}{...}
{title:Options}
{phang}
{opt level(#)}; see {helpb estimation options##level():[R] estimation options}.
{phang}
{opt nome} specifies the NOME (no measurement error in the genotype-phenotype [SNP-exposure]
associations) assumption.
{phang}
{opt nosave} specifies that the density of the IV estimates and column vector
of IV estimates should not be saved in Mata. If not specified these are saved
in Mata as mrmodal_densityiv and mrmodal_g respectively.
{phang}
{opt phi(#)} specifies the parameter phi which is used in the calculation of
the bandwidth for the density estimation. Default is phi = 1, other values
commonly chosen are 0.25 and 0.5.
{phang}
{opt reps(#)} specifies the number of bootstrap replications for obtaining the
standard error. The default is 1000 replications.
{phang}
{opt seed(#)} specifies the initial value of the random-number seed.
The default is the current random-number seed. Specifying {opt seed(#)} is the
same as typing {cmd:set seed} {it:#} before issuing the command;
see {helpb set_seed}.
{phang}
{opt weighted} weight the instrumental variable estimates.
{marker examples}{...}
{title:Examples}
{pstd}Using the data provided by {help mrmodal##do:Do et al. (2013)}.{p_end}
{pstd}Setup{p_end}
{phang2}{cmd:.} {stata "use https://raw.github.com/remlapmot/mrrobust/master/dodata, clear"}{p_end}
{pstd}Select observations ({it:p}-value with exposure < 10^-8){p_end}
{phang2}{cmd:.} {stata "gen byte sel1 = (ldlcp2 < 1e-8)"}{p_end}
{pstd}Investigate what is a good value of phi to use (we want a smooth density plot){p_end}
{phang2}{cmd:.} {stata "mrmodalplot chdbeta chdse ldlcbeta ldlcse if sel1==1"}{p_end}
{pstd}Simple mode estimator{p_end}
{phang2}{cmd:.} {stata "mrmodal chdbeta chdse ldlcbeta ldlcse if sel1==1"}{p_end}
{pstd}Simple mode estimator with reproducible standard error{p_end}
{phang2}{cmd:.} {stata "mrmodal chdbeta chdse ldlcbeta ldlcse if sel1==1, seed(12345)"}{p_end}
{pstd}Weighted mode estimator{p_end}
{phang2}{cmd:.} {stata "mrmodal chdbeta chdse ldlcbeta ldlcse if sel1==1, weighted"}{p_end}
{pstd}Simple mode estimator with NOME assumption{p_end}
{phang2}{cmd:.} {stata "mrmodal chdbeta chdse ldlcbeta ldlcse if sel1==1, nome"}{p_end}
{pstd}Weighted mode estimator with NOME assumption{p_end}
{phang2}{cmd:.} {stata "mrmodal chdbeta chdse ldlcbeta ldlcse if sel1==1, weighted nome"}{p_end}
{marker results}{...}
{title:Stored results}
{pstd}
{cmd:mrmodal} stores the following in {cmd:e()}:
{synoptset 20 tabbed}{...}
{p2col 5 20 24 2: Scalars}{p_end}
{synopt:{cmd:e(k)}}number of instruments{p_end}
{synopt:{cmd:e(phi)}}value of phi{p_end}
{synopt:{cmd:e(reps)}}number of (bootstrap) replications{p_end}
{synoptset 20 tabbed}{...}
{p2col 5 20 24 2: Macros}{p_end}
{synopt:{cmd:e(cmd)}}{cmd:mrmodal}{p_end}
{synopt:{cmd:e(cmdline)}}command as typed{p_end}
{synoptset 20 tabbed}{...}
{p2col 5 20 24 2: Matrices}{p_end}
{synopt:{cmd:e(b)}}coefficient vector{p_end}
{synopt:{cmd:e(V)}}variance-covariance matrix of the estimates{p_end}
{marker references}{...}
{title:References}
{marker do}{...}
{phang}
Do et al. Common variants associated with plasma triglycerides and risk
for coronary artery disease. Nature Genetics, 2013, 45, 1345-1352.
{browse "https://dx.doi.org/10.1038/ng.2795":DOI}
{p_end}
{marker hartwig}{...}
{phang}
Hartwig FP, Davey Smith G, Bowden J.
Robust inference in two-sample Mendelian randomisation via the zero modal
pleiotropy assumption. International Journal of Epidemiology, 2017, 46, 6, 1985-1998.
{browse "https://doi.org/10.1093/ije/dyx102":DOI}
{marker author}{...}
{title:Author}
INCLUDE help mrrobust-author