Post by jonic on Sept 2, 2016 14:45:23 GMT
Multiple GRMs (one for the whole cohort, and one just capturing familial relationships) can be used to capture SNP-heritability in family data, as detailed on this forum (gcta.freeforums.net/thread/241/gcta-greml-analysis-family-data) and in Zaitlen et al, 2013 (journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003520).
Can this be incorporated into an MLMA analysis (within or outside of GCTA?)
Naively, I can see three options, but I am unsure which is the best (or if any of them make sense!):
Can this be incorporated into an MLMA analysis (within or outside of GCTA?)
Naively, I can see three options, but I am unsure which is the best (or if any of them make sense!):
- Using the GRM for the whole cohort (seems vulnerable to confounding from shared environmental factors)
- Fitting both GRMs in the model (straightforward, but not convinced this appropriately captures the gross shared genomic relationship)
- Performing some kind of subtraction of the familial GRM from the whole cohort GRM (most likely through generating breeding values from each GRM first), and fitting the result as a random effect capturing the gross genetic relationship (akin to the described method for estimating heritability, but not straightforward without performing the MLMA outside of GCTA).
