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| arrayAppend | Append two arrays by adding new data to top array |
| BayesAB | Estimte SNP Effects by MCMC - Bayes (A and B) - beta |
| BayesCpi | Estimte SNP Effects by MCMC - Bayes C and Cpi - beta |
| GetHCS | Check SNP genotypes and exclude redundant SNPs |
| getMAF | Return frequency of the minor allele of a SNP |
| is.hwEq | Check a SNP for Hardy-Weinberg equilibrium |
| is.identical | Check two SNPs for near identity across genotyped samples |
| read.findhap | Read the output of Paul Vanraden's findhap, 'genotypes.filled' |
| snpRecode | Recode a matrix of SNP genotypes as 0, 1, and 2 |
| snpSelect | Select genotyped individuals and SNPs based on call rate, heterozygosity, HW equilibrium, or minor allele frequency. |
| toArray | Turn Illumina's Genome Studio 'Final Report' file into an array |