Post by ab99 on Mar 20, 2015 15:59:27 GMT
Hi,
We are trying to do quantitative trait prediction in an independent cohort using GCTA. We followed GCTA's online manual and did the following:
a) Use "--blup-snp" to calculate the BLUP solutions for the SNP effects;
b) Predict the total genetic effect of individuals in an independent sample by PLINK --score option (i.e., add up all SNPs' effects together)
Two quick questions:
1) I believe the "total genetic effect of individuals" as estimated by "PLINK --score" does not include the effects of covariates. Am I right?
2) If I am right with 1), then the question is whether there is a way to add the effects of covariates into the predictor. Ultimately, we want to get the best prediction that we can, and often the covariates can contribute significantly.
Thank you!
ab99
We are trying to do quantitative trait prediction in an independent cohort using GCTA. We followed GCTA's online manual and did the following:
a) Use "--blup-snp" to calculate the BLUP solutions for the SNP effects;
b) Predict the total genetic effect of individuals in an independent sample by PLINK --score option (i.e., add up all SNPs' effects together)
Two quick questions:
1) I believe the "total genetic effect of individuals" as estimated by "PLINK --score" does not include the effects of covariates. Am I right?
2) If I am right with 1), then the question is whether there is a way to add the effects of covariates into the predictor. Ultimately, we want to get the best prediction that we can, and often the covariates can contribute significantly.
Thank you!
ab99
