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Note that since we are not using the individuals with missing trait values for the polygenic calculations, we essentially are performing a complete case (CC) analysis.
In Part II, FAM-MDR obviously does not use missing new trait values, whether these are due to missing trait values or missing main effects/covariates adjusted for.
Individuals with missing trait values are used in FAM-MDR Part I only when they are useful for deriving the relationship matrix, but never for the polygenic calculations themselves.
When the number of markers is large, FAM-MDR relies on the genomic kinship matrix and there is no need to keep individuals with missing trait values in the analysis.
Missing trait data (0 4.5% of data) were imputed by default parameter settings which uses an average of three nearest neighbor values.
at-Statistic tdf with df degrees of freedom for estimation of difference in means (employing a linear model on Blom-transformed trait; small differences in degrees of freedom are due to low percentages of missing trait values).
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We relegate their existence to a checklist of missing traits: no limbs, muscles, nerves, or organs, and none of the tiger's fearful symmetry.
In 2,768 participants MetS was not definable because of missing traits.
The interest in using the RRM with Gibbs sampling rather than, e.g., REML or a multiple-trait model, was the fact that, on one hand, the relationship matrix needed to be stored just once (in contrast to regular REML, for instance), and on the other hand, no "data augmentation" of missing traits was needed with the RRM, in contrast to using regular Gibbs sampling with a multiple-trait model.
In this latter case, the solution would likely be to exclude the patient from the sample, while in the case of geometric morphometrics, it may be acceptable to give to the anatomical trait a "zero" value and include it in calculations, if the missing anatomical trait is not the main clinical question to solve.
Missing new trait values are also not included in the permutation procedure.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com