SNP effects on the residual (unique) variance

[GenEpiLab]

Hi, thank you so much for this resource. 

I would like to know how to identify SNPs associated with unique variance beyond the common factor. If I have three variables for simplicity's sake, is this correct?

model <- "F1 =~ VAR1 + VAR2 + VAR3

VAR1 ~~ SNP

VAR2 ~~ SNP

VAR3 ~~ SNP

"

and then teh same terms in userGWAS (i.e., sub = c("VAR1 ~~ SNP", "VAR2 ~~ SNP", "VAR3 ~~ SNP"))?

Thanks!

Mary

[Elliot Tucker-Drob]

Such a model is not identified but the Qsnp statistic will be very useful here and you can perform post hoc analyses to identify the pathways that likely drive Qsnp for a particular variant as we explain here (see supplement in particular):

de la Fuente, J., Davies, J., Grotzinger, A. D., Tucker-Drob, E. M., & Deary. (2020). A general dimension of genetic sharing across diverse cognitive traits inferred from molecular data. Nature Human Behaviour. [de la Fuente & Davies contributed equally to this work; Tucker-Drob & Deary jointly directed this work] Link Supplements

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