Clipping one of two markers which are located very close to each other

 

As the result of the experiments that were performed,  we  found that clipping one of two markers that the distance between them is signed by a small recombination value doesn't influence the LOD score, regardless to the location of the marker on the map. We define the bound for the recombination value as THETA_BOUND , and  can clip the markers with recombination value lower than THETA_BOUND.

Experimental results for measuring the influence of clipping close markers on the LOD score:

 

  

datafile40_70_9_0.01.dat, pedfile40_70_9_0.01.dat, THETA_BOUND = 0.005

Num Loci

Num People

Exact LOD score

Approx LOD score

error rate

RATIO_BOUND

40

70

-44.808750

-44.808070

0%

0.3

40

70

-44.808750

-43.267929

3.4%

0.2

40

70

-44.808750

-48.138169

7.4%

0

 

datafile20_20_7_0.01.dat, pedfile20_20_7_0.01.dat, THETA_BOUND = 0.005

Num Loci

Num People

Exact LOD score

Approx LOD score

error rate

RATIO_BOUND

20

20

0.147506

0.144640

1.9%

0.3

20

20

0.147506

0.159113

7.9%

0.2

20

20

0.147506

0.014602

90%

0

 

 

datafile40_70_9_rand.dat, pedfile40_70_9_rand.dat, RATIO_BOUND = 0.3

Num Loci

Num People

Exact LOD score

Approx LOD score

error rate

THETA_BOUND

40

70

-47.032776

-47.032776

0%

0.001

40

70

-47.032776

-45.570694

3%

0.005

40

70

-47.032776

-45.566095

3.1%

0.008

 

datafile20_20_7_rand.dat, pedfile20_20_7_rand.dat, INFO_DISTANCE_BOUND = 0.3

Num Loci

Num People

Exact LOD score

Approx LOD score

error rate

THETA_BOUND

20

20

0.113474

0.109877

3.1%

0.001

20

20

0.113474

0.098526

13.1%

0.005

20

20

0.113474

0.183514

61.7%

0.008

 

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