family-based association: are the genotype and phenotype standardized?

[Gabriele Sgarlata]

Hi there,

I have a quick question regarding family-based association.

When running --qfam, does plink mean-center and variance-scale the phenotype and the genotype? Just to understand whether the effect sizes for each SNPs are standardized or not.

Thank you in advance,

Gabriele 

[Chris Chang]

The documentation makes no mention of standardization.  The commands which do perform automatic variance-standardization (--make-grm-..., --pca) mention this prominently in their documentation.

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[Gabriele Sgarlata]

Hi Chris,

Thank you for getting back.

I know that the PLINK documentation does not mention standardization for the --qfam method (as also the two papers you cite), this is why I wanted things to be clear in mind, since the interpretation of the effect sizes can be quite different in the two cases.

I had already looked at the automatic variance-standardization in these other approaches, but this is not what I am interested in, since I am planning to perform a simple family-association analysis:

plink --bfile $input --qfam mperm = 100000

Thanks

Gabriele