Hi everyone,
Please...
In order to look for for a difference in genetic (GWAS' SNPs obtained previously in my population study) risk contribution for an interested phenotype, I´ve been using a weighted method, calculating an average GRS per allele from each SNP for each individual.
However I blocked now. I don´t know if I should use the OR values from the previously GWAS SNPs, or if I should do a logistic regression test with the risk all count alleles per SNP in all my sample in order to obtain the weight (OR) values.
Any help?
Thank you so much!
Don't quite understand the question - do you have two different datasets:
If that is the case, you should weight by the OR from the original GWAS - PLINK can do this (--score). Alternatively, you could use PRSice software, which does the whole thing in a handy R wrapper (www.prsice.info)