Grouping LOD Score Threshold

Use this option to specify a threshold for the grouping value of the LOD score when using the Minimum Recombination Grouping method. This is used as an additional criteria to stop joining marker groups in the Minimum Spanning Tree optimization algorithm used in the Minimum Recombination Grouping method.

Linkage groups areformed by assigning a marker to a group only if the marker has both a recombination fraction less than or equal to the Grouping Recombination Fraction Threshold parameter value and LOD score greater than or equal to this specified value with at least one marker already in the linkage group. If a marker is not linked to any markers in a linkage group based on this value, then that marker is placed in a new linkage group.

This value and the Grouping Recombination Fraction Threshold parameter value will determine the number of linkage groups.

The Minimum Spanning Tree algorithm builds a tree connecting markers with edges proportional to their recombination fraction (the markers with the smallest recombination values will be joined first). Once the minimum length of a potential edge between markers becomes smaller than the specified LOD threshold or the recombination fraction becomes larger than the Grouping Recombination Fraction Threshold value or the Minimum Number of Linkage Groups parameter value is surpassed, the algorithm will stop forming edges between markers and linkage groups will be then comprised of markers with connected edges.

If you want the formation of linkage groups to be based solely on the LOD grouping threshold specified, you should enter a very high (e.g. >= 0.5) value in the Grouping Recombination Fraction Threshold parameter field and a value of 1 in the Minimum Number of Linkage Groups parameter field.

Note: If a Framework Linkage Group Variable is specified, the Minimum Number of Linkage Groups is automatically set to the number of defined framework groups.