jonic
New Member
Posts: 7
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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!): - 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).
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Post by Jian Yang on Sept 8, 2016 5:19:10 GMT
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jonic
New Member
Posts: 7
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Post by jonic on Sept 12, 2016 12:04:50 GMT
Thanks - I hadn't come across the --mlma-subtract-grm flag, that looks like a very useful addition!
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