Dear all,
I ran LDSC and a 2-factor Genomic SEM model including lymphoma subtypes and autoimmune diseases.
The LDSC results show limited genetic correlation between lymphomas and autoimmune diseases, but stronger correlations within each disease group. The 2-factor Genomic SEM model similarly suggests two largely separate latent factors, with a very small factor correlation, around -0.04.
I would now like to run per-SNP analyses. Ideally, I would use userGWAS() for the full 2-factor model, but I have not been able to get this working.
Since my main interest is lymphoma, would it be defensible to instead run a per-SNP common factor GWAS using only the lymphoma traits (this works fine in my data)?
So the analysis would be:
-
LDSC across lymphoma and autoimmune diseases
-
2-factor Genomic SEM showing minimal correlation between factors
-
Lymphoma-only common factor GWAS as the per-SNP follow-up
Does this seem like a reasonable strategy, or would it be problematic to move from the full 2-factor model to a lymphoma-only per-SNP model?
I am having trouble decifering if this would be seen as problematic.
Thank you for a great course!
Kind regards,
Jojo