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maineff1
2012 Aug 24
0
A question about GRAMMAR calculations in the FAM_MDR algorithm
...r (k in 1:nsnps){
SNPS[,k] = allelic(k)
}
SNPS = as.data.frame(SNPS)
SNPS[SNPS==-1] = NA
# GRAMMAR calculations
# here one has to include main effect and/or covariate adjustments in the
polygenic model statement
pkin = kinship(pedigree[,2],pedigree[,3],pedigree[,4])
maineff1 = as.factor(SNPS[,1])
maineff2 = as.factor(SNPS[,2])
Yfit =
polygenic(trait~maineff1+maineff2,pkin,simulation.GenABEL,trait.type="gaussian")
resi = Yfit$pgresidualY
When I calculated the GRAMMAR and ran the command, "*Yfit =
polygenic(trait~maineff1+maineff2,pkin,simulation.GenABEL,trait.type="gaussian&q...