hap.freq: Estimation of Haplotype Frequencies with Two SNPs
In IFP: Identifying Functional Polymorphisms

Description Usage Arguments Value See Also Examples

EM computation of haplotype frequencies with two SNPs. The computation is relied on the package"haplo.stats".

1	hap.freq(geno)

geno

matrix of alleles, such that each locus has a pair of adjacent columns of alleles, and the order of columns corresponds to the order of loci on a chromosome. If there are K loci, then ncol(geno) = 2*K. Rows represent the alleles for each subject. Each allele shoud be represented as numbers (A=1,C=2,G=3,T=4).

matrix of haplotype frequencies consisted of two alleles from each SNP. These alleles are the same ones computed for frequency using the function "allele.freq".

allele.freq

1
2
3

 data(apoe)
 hap.freq(apoe7)
 hap.freq(apoe)

           [,1]       [,2]       [,3]         [,4]         [,5]         [,6]
[1,]         NA 0.10946794 0.51886476 1.521951e-01 3.186900e-01 8.718718e-02
[2,] 0.10946794         NA 0.05473703 5.824397e-02 1.439386e-02 1.794180e-02
[3,] 0.51886476 0.05473703         NA 1.111651e-02 4.270833e-01 5.325158e-02
[4,] 0.15219513 0.05824397 0.01111651           NA 4.738558e-09 1.100443e-06
[5,] 0.31868996 0.01439386 0.42708333 4.738558e-09           NA 5.311645e-09
[6,] 0.08718718 0.01794180 0.05325158 1.100443e-06 5.311645e-09           NA
[7,] 0.63155906 0.06621117 0.57774191 2.311276e-01 4.270833e-01 1.145832e-01
           [,7]
[1,] 0.63155906
[2,] 0.06621117
[3,] 0.57774191
[4,] 0.23112759
[5,] 0.42708333
[6,] 0.11458317
[7,]         NA
            [,1]       [,2]         [,3]        [,4]         [,5]         [,6]
 [1,]         NA 0.96875000 7.187500e-01 0.125000000 6.666667e-01 2.776080e-01
 [2,] 0.96875000         NA 7.083333e-01 0.125000000 6.562500e-01 2.812500e-01
 [3,] 0.71874999 0.70833333           NA 0.109467830 5.188634e-01 1.521996e-01
 [4,] 0.12500000 0.12500000 1.094678e-01          NA 5.473703e-02 5.824531e-02
 [5,] 0.66666666 0.65625000 5.188634e-01 0.054737028           NA 1.111650e-02
 [6,] 0.27760797 0.28125000 1.521996e-01 0.058245309 1.111650e-02           NA
 [7,] 0.95833333 0.96875000 7.015592e-01 0.104166667 6.666667e-01 2.604167e-01
 [8,] 0.04166667 0.04166667 4.166652e-02 0.017831135 2.373284e-09 6.958270e-03
 [9,] 0.42708333 0.41666667 3.186850e-01 0.014393827 4.270833e-01 3.645747e-09
[10,] 0.01041667 0.01041667 1.943822e-08 0.000000000 0.000000e+00 1.041665e-02
[11,] 0.96875000 0.97916667 7.187500e-01 0.125000000 6.562500e-01 2.812500e-01
[12,] 0.09375000 0.11458333 8.689737e-02 0.017942819 5.325265e-02 1.054857e-06
[13,] 0.95833333 0.96875000 7.015583e-01 0.125000000 6.458333e-01 2.812500e-01
[14,] 0.86458333 0.87500000 6.318523e-01 0.066211034 5.777375e-01 2.311267e-01
[15,] 0.95833333 0.96875000 7.014876e-01 0.116205182 6.459113e-01 2.776095e-01
[16,] 0.03125000 0.03125000 1.682065e-02 0.007059729 3.125000e-02 0.000000e+00
            [,7]         [,8]         [,9]        [,10]      [,11]        [,12]
 [1,] 0.95833333 4.166667e-02 4.270833e-01 1.041667e-02 0.96875000 9.375000e-02
 [2,] 0.96875000 4.166667e-02 4.166667e-01 1.041667e-02 0.97916667 1.145833e-01
 [3,] 0.70155922 4.166652e-02 3.186850e-01 1.943822e-08 0.71874999 8.689737e-02
 [4,] 0.10416667 1.783113e-02 1.439383e-02 0.000000e+00 0.12500000 1.794282e-02
 [5,] 0.66666666 2.373284e-09 4.270833e-01 0.000000e+00 0.65625000 5.325265e-02
 [6,] 0.26041667 6.958270e-03 3.645747e-09 1.041665e-02 0.28125000 1.054857e-06
 [7,]         NA 4.166667e-02 4.270833e-01 1.041667e-02 0.96875000 1.145833e-01
 [8,] 0.04166667           NA 1.767283e-07 1.041667e-02 0.04166667 4.166667e-02
 [9,] 0.42708333 1.767283e-07           NA 0.000000e+00 0.41666723 6.333845e-09
[10,] 0.01041667 1.041667e-02 0.000000e+00           NA 0.01041667 1.041667e-02
[11,] 0.96875000 4.166667e-02 4.166672e-01 1.041667e-02         NA 1.145833e-01
[12,] 0.11458333 4.166667e-02 6.333845e-09 1.041667e-02 0.11458333           NA
[13,] 0.95833333 4.166667e-02 4.270833e-01 1.041667e-02 0.96875000 9.375000e-02
[14,] 0.87356867 4.166667e-02 4.270833e-01 1.041667e-02 0.87500000 1.145832e-01
[15,] 0.95833333 4.166667e-02 4.270833e-01 1.041667e-02 0.96875000 9.375000e-02
[16,] 0.03125000 0.000000e+00 3.124996e-02 0.000000e+00 0.03125000 0.000000e+00
           [,13]      [,14]      [,15]       [,16]
 [1,] 0.95833333 0.86458333 0.95833333 0.031250000
 [2,] 0.96875000 0.87500000 0.96875000 0.031250000
 [3,] 0.70155830 0.63185226 0.70148764 0.016820646
 [4,] 0.12500000 0.06621103 0.11620518 0.007059729
 [5,] 0.64583333 0.57773754 0.64591131 0.031250000
 [6,] 0.28125000 0.23112675 0.27760949 0.000000000
 [7,] 0.95833333 0.87356867 0.95833333 0.031250000
 [8,] 0.04166667 0.04166667 0.04166667 0.000000000
 [9,] 0.42708333 0.42708333 0.42708333 0.031249963
[10,] 0.01041667 0.01041667 0.01041667 0.000000000
[11,] 0.96875000 0.87500000 0.96875000 0.031250000
[12,] 0.09375000 0.11458317 0.09375000 0.000000000
[13,]         NA 0.86458333 0.95833333 0.031250000
[14,] 0.86458333         NA 0.87356688 0.011687985
[15,] 0.95833333 0.87356688         NA 0.031250000
[16,] 0.03125000 0.01168799 0.03125000          NA