A1/A2: Returns the letter for the A1/A2 alleles for the chip object, e.g, 'A','C','G','T', etc Only if these are annotated internally, or else a vector of NAs
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)# S4 method for ChipInfo
A1(x)
A2(x)
# S4 method for ChipInfo
A2(x)
A1(x) <- value
# S4 method for ChipInfo
A1(x) <- value
A2(x) <- value
# S4 method for ChipInfo
A2(x) <- value
a ChipInfo object
new allele codes, e.g, A,C,G,T
character vector of allele codes (or NAs)
A1<-: updates the ChipInfo object specified with new allele codes for the 'A1' slot
A2<-: updates the ChipInfo object specified with new allele codes for the 'A2' slot