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Post by Mark Dwain on Apr 3, 2014 16:58:33 GMT
Hi,
I want to use a pedigree (stored in a PLINK fam file) as a GRM for GCTA. I've computed one using the kinship2 R package, and am converting it into text-based input for GCTA. I noticed one of the requirements for the input format is the number of non-missing SNPs that went into the calculation --- how is this number used by GCTA? Will it affect my results since my choice will be arbitrary in this case?
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Post by Jian Yang on Apr 4, 2014 13:15:11 GMT
You can put any non-zero number. It won't affect your result unless you use the --grm-adj option.
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