A1<-/A2<-: Allows user to set the allele codes for each SNP of the chip object, e.g, A,C,G,T,K, etc. If you are using allele codes this is likely to necessary as each genotyping produces a different set of allele codes. If using in conjunction with snpStats, remember that allele codes are always flipped to be alphabetical, so the reference allele is the later letter in the alphabet. Note, assignment to A2 needs to be done separately.
A1(x)
"A1"(x)
A2(x)
"A2"(x)
A1(x) <- value
"A1"(x) <- value
A2(x) <- value
"A2"(x) <- value