MRInput Class

An object containing the four vectors of summary statistics required to calculate Mendelian randomization estimates.

Details

The beta-coefficients are assumed to be estimated for uncorrelated (independent) genetic variants, although a correlation matrix can be specified if the variants are correlated in their distributions. We also assume that the beta-coefficients for associations with the exposure and with the outcome are uncorrelated (corresponding to a two-sample Mendelian randomization analysis), although correlation between associations with the exposure and with the outcome generally have little impact on causal estimates or standard errors. Estimates can either be specified by the user, or extracted from the PhenoScanner tool.

Slots

betaX

A numeric vector of beta-coefficient values for genetic associations with the first variable (often referred to as the exposure, risk factor, or modifiable phenotype).

betaY

A numeric vector of beta-coefficient values for genetic associations with the second variable (often referred to as the outcome). For a disease outcome, the beta coefficients are log odds estimates from logistic regression analyses.

betaXse

The standard errors associated with the beta-coefficients in betaX.

betaYse

The standard errors associated with the beta-coefficients in betaY.

correlation

The matrix of correlations between genetic variants. If this variable is not provided, then we assume that genetic variants are uncorrelated.

exposure

The name of the exposure variable.

outcome

The name of the outcome variable.

snps

The names of the genetic variants (SNPs) included in the analysis. The slots exposure, outcome, and snps are not required, but may be useful for keeping track of various MRInput objects. They are also used by the mr_plot function.

effect_allele

The name of the effect allele for each SNP. The beta-coefficients are the associations with the exposure and outcome per additional copy of the effect allele.

other_allele

The name of the non-effect allele.

eaf

The expected allele frequencies (numeric). The slots effect_allele, other_allele, and eaf are neither required, nor currently used in the MendelianRandomization package. They are included for future compatibility with the MR-Base suite of functions.