Clipping  markers which are located far from the iterated locus

As the result of the experiments that were performed,  we found that clipping  until half of the total number of markers doesn't influence the LOD score when we clip each time the marker farthest from the iterated locus. We also found that when the iterated locus is the first or the last  on the map, we can clip farthest markers until 3/4 of the total number of markers without influence on the LOD score. The maximum distance from the varied locus to markers that influence the final LOD score is various for different input data files, as well as the number of those markers.

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

• For the experimental needs we define ratio = (number of clipped markers)/(total number of loci in the file)

• Here we'd like to show the influence on the LOD score of clipping  different amount of farthest markers  from the same file. It can be seen that when the ratio <0.5 in the regular case, and when the ratio <0.75 in  case the Varied Locus is the first or the last locus on the map the error rate is zero.

datafile40_70_9.dat, pedfile40_70_9.dat, Varied Locus = 20

 Exact LOD score Approx LOD score error rate ratio Num Loci Num People 40 70 -14.013844 -14.013844 0% 19/40 40 70 -14.013844 -17.382109 24% 23/40 40 70 -14.013844 -18.662389 33% 26/40

datafile40_70_9_1.dat, pedfile40_70_9_1.dat, Varied Locus = 1

 Exact LOD score Approx LOD score Num Loci Num People
 40 70 -2.33107 -2.33107 0% 29/40 40 70 -2.33107 -2.25911 3% 34/40 40 70 -2.33107 -2.78137 19.3% 36/40

datafile76_20_7.dat, pedfile76_20_7.dat, Varied Locus = 38

 Exact LOD score Approx LOD score error rate ratio Num Loci Num People 76 20 -11.597888 -11.597888 0% 37/76 76 20 -11.597888 -13.214128 13.9% 45/76 76 20 -11.597888 -13.349134 15% 58/76

datafile76_20_7_1.dat, pedfile76_20_7_1.dat, Varied Locus = 1

 Exact LOD score Approx LOD score error rate ratio Num Loci Num People 76 20 -2.885523 -2.885523 0% 56/76 76 20 -2.885523 -2.885523 0% 65/76 76 20 -2.885523 -2.819683 2% 73/76

The following graphs represent the  LOD error rate as a function of  the percent of clipped markers (farthest markers). Error rate increases when the number of clipped markers grows up. The way it increases is various for different input files. However, it can be seen that clipping lower than 50% of total number of markers, in the case of  "iterated locus is in the middle of the map", and lower that 75% of total number of markers , in the case of "iterated locus is the first or the last on the map",  gives LOD error rate = 0 for different input files. Each graph represents LOD error rate for two different input files according to experimental results mentioned above.

To see the graph for the case of "iterated locus is in the middle of the map" click here.

To see the graph for the case of "iterated locus is the first or the last on the map" click here.

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