ab99
New Member
Posts: 8
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Post by ab99 on Aug 12, 2014 19:55:01 GMT
Hi,
I hope to get a confirmation about how the genetic relationship matrix (GRM) is estimated.
Based on Yang et al. AJHG (2011), the jk'th element of GRM (the genetic relationship between individuals j and k) can be calculated by:
Ajk = sum(over all SNPs i)[wij * wik]/N
where wij is the standardized genotype dosage defined by: (xij-2pi)/sqrt(2pi(1-pi)), and N is the total number of SNPs.
My questions:
1) Does GCTA use the above formula to estimate Ajk?
2) My understanding is that Ajk is asymptotically the correlation coefficient between the two standardized genotype dosage vectors for individuals j and k. Am I right?
3) If the answer to Q2 is yes, then majority of Ajk values should be between (-1, 1), and most likely between (0,1). However, in our real data analysis, we see a following summary for diagonal values: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.8651 0.9198 0.9463 1.0050 1.0070 18.5600 We observe quite some values > 1, with maximum at 18. Why is that? Are there anything I should be concerned about?
Thank you!
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Post by Jian Yang on Aug 16, 2014 12:09:50 GMT
Re 1) Yes. Re 2) No. The GRM method is derived from equating the SNP-based model to an individual-based model (see Yang et al. 2010 Nat Genet).
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ab99
New Member
Posts: 8
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Post by ab99 on Sept 16, 2014 14:30:21 GMT
Re 1) Yes. Re 2) No. The GRM method is derived from equating the SNP-based model to an individual-based model (see Yang et al. 2010 Nat Genet). Hi Jian, Thanks for your reply! I am wrong on this then. I will read your Nat Genet paper and come back to you if I have further questions. Thanks again, ab99
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