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Post by cgte88586 on Jan 24, 2016 6:40:25 GMT
My input bfile has 269308 SNPs, the N in out.grm.N.bin is 269050 (258 are missing). Why does that happen when no filter is applied?
My code is
gcta64 --bfile "data"
--make-grm --out out
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Post by Jian Yang on Jan 26, 2016 6:21:40 GMT
This is because there are missing genotypes for each individual. If you read the GRM in R using the code "grm=ReadGRMBin(out, AllN=TRUE)", you could see "N" for each element of the GRM.
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Post by cgte88586 on Jan 31, 2016 23:36:06 GMT
This is because there are missing genotypes for each individual. If you read the GRM in R using the code "grm=ReadGRMBin(out, AllN=TRUE)", you could see "N" for each element of the GRM. Thank you for pointing that out, Jian. That makes perfect sense now! The number 269050 I was looking at is actually 'the # of SNPs for calculating the first element of the GRM'. |
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