| Class | Analysis and data manipulation command |
| Name | dis |
| Arguments | [<marker locus 1> [<marker locus 2> [...<marker locus N> [<trait locus>]]]] |
Estimates frequencies of haplotypes based on individuals with two informative parents or no informative parents. For pairs of multiallelic markers (6 or more alleles), only the former group is used. In the informative parent-offspring triads, the loci are assumed to be tightly linked, so that four parental haplotypes may be inferred, but this can be turned off (set hrec).
If no markers are specified, the sequence of pairs of markers in the list of loci is produced (ie marker1 with marker2, marker2 with marker3...). If one marker is specified, then the pairing of all other markers with this index marker is analysed.
For pairs of markers with few alleles, information from both phased and unphased genotypes is combined using an EM-fitted log-linear model, which can also deal with X-linked data.
If three or more markers are specified, or two or more markers along with a trait, the genotypes are all treated as if unphased (and X-linked data is not handled). The same log-linear modelling framework is used.
When a trait is specified, the haplotype frequencies within each trait category (two if a binary trait, as many levels as observed for a quantitative trait) are calculated, along with a chi-square testing equality of marker haplotype frequencies across categories.
If exactly two numbers are given, then these are assumed to be the number of alleles at two loci, and genotype counts may be entered at the command line.
Two likelihood ratio tests are provided for the two locus case. The first tests the adequacy of the intragametic association model ie absence of population stratification type effects. The other tests if there is significant intragametic association (ie D or r ≠ 0).
If the r2 is given, the pairwise r2 matrix for all pairs of active markers is printed. The dpr gives the matrix of Hedrick weighted D' for all pairs of active markers.
Example:
>> dis
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Inter-marker allelic association analysis
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Marker 1 Marker 2 N mean D' r2 Chi-sq df asy P
---------- ---------- ---- ------- ----- ------ --- ------
E366K rs1122629 3564 0.872 0.016 85.8 1 0.0000 LD ***
rs1122629 rs1303 3540 0.252 0.023 95.0 1 0.0000 LD ***
>> set ple 2
>> dis E366K rs1122629
---------------------------------------------------
Inter-marker allelic association analysis
---------------------------------------------------
Assoc for locus "E366K " c. locus "rs1122629 "
---------------------------------------------------
Modelling 10 phased genotypes (N= 628) and 9 unphased genotypes (N= 2936).
Unphased Genotypes Observed Expected Deviance
1/1 1/1 0. 0.0 -0.0
1/1 1/2 0. 0.2 -0.3
1/1 2/2 2. 1.1 0.8
1/2 1/1 6. 4.0 1.0
1/2 1/2 58. 61.2 -0.4
1/2 2/2 59. 54.2 0.7
2/2 1/1 753. 745.4 0.3
2/2 1/2 1397. 1406.5 -0.2
2/2 2/2 661. 663.5 -0.1
Phased Genotypes Observed Expected Deviance
1 1; 1 1 0. 0.0 -0.0
1 1; 2 1 0. 0.0 -0.1
1 1; 2 2 0. 0.2 -0.4
2 1; 1 1 0. 0.8 -1.1
2 1; 1 2 11. 12.3 -0.3
2 2; 1 1 152. 159.4 -0.6
2 1; 2 1 0. 0.8 -1.0
2 1; 2 2 10. 11.6 -0.4
2 2; 2 1 313. 300.8 0.7
2 2; 2 2 142. 141.9 0.0
Haplotype Prop 95% CL D D'
----------------------------------------------------
A C 0.0013 0.0007--0.0025 -0.0092 -0.8724
A T 0.0194 0.0165--0.0229 0.0092 0.8724
G C 0.5039 0.4893--0.5188 0.0092 0.8724
G T 0.4754 0.4612--0.4900 -0.0092 -0.8724
Number of genotypes used = 3564
LD Model LR Chi-square = 7.57 (df= 14, P=0.9103)
LR Chi-square (D=0) = 85.79 (df= 1, P=0.0000)
Hedrick weighted mean D' = 0.8724
r-squared = 0.0165
>> dis 2 2
9 genotype counts> 91 147 85 32 78 75 5 17 7
Modelling 9 unphased genotypes (N= 537).
Haplotype Prop 95% CL D D'
----------------------------------------------------
1 1 0.3822 0.3503--0.4169 0.0234 0.2231
1 2 0.3916 0.3594--0.4266 -0.0234 -0.2231
2 1 0.0815 0.0664--0.1001 -0.0234 -0.2231
2 2 0.1448 0.1244--0.1684 0.0234 0.2231
Number of genotypes used = 537
LD Model LR Chi-square = 12.81 (df= 5, P=0.0252)
LR Chi-square (D=0) = 8.01 (df= 1, P=0.0046)
Hedrick weighted mean D' = 0.2231
r-squared = 0.0126
See also:
| set hre | Assume zero recombination for phased LD model |
| write haploview | write Haploview pedigree file |
| write locus haploview | write Haploview info file |
| haplotypes | haplotypes for pairs of SNPs |
| << (mds) | Up to index | >> (neff) |