the coefficient of the causal SNP for logistic model
case.sub
case subjects, two columns for two haplotypes
ctl.sub
control subjects, two columns for two haplotypes
lib.sub
the alleles library contains allele sequences for those only appear in the case and control samples
lib.sub.names
the corresponding names of the alleles
risk.type
risk.type="AA": simulated from given amino acid position as shown in matrix lib.sub, use risk.inx to input position
risk.type="allele":simulated from given risk alleles, use risk.names=c("301", "302") to specified those alleles
risk.inx
the given amino acid position
risk.names
allele names
min.count
use to calculate the warning if the selected alleles have too small frequencies