Description Usage Arguments Details Value See Also
Calculates the total, mean and individual differences between the observed and estimated distances from all loci and their nearest neighbours with non-zero LOD scores.
1 | calc.nnfit(distmap, lodmap, estmap)
|
distmap |
Symmetric matrix of pairwise inter-marker distances with columns and rows corresponding to the estimated map order. |
lodmap |
Symmetric matrix of pairwise lod scores with columns and rows corresponding to the estimated map order. |
estmap |
Vector of estimated marker positions. |
The nearest neighbour fit for a marker is the sum of the difference between the observed and estimated distances between the marker and its nearest informative neighbour. A neighbour is informative if the LOD score for the inter-marker distance is greater than zero. This function calculates the nearest neighbour fit for each marker and returns the fit for each point and the sum of all the fits.
A list with the elements:
fit |
Sum of the nearest neighbour fits over all markers. |
pointfits |
Vector of nearest neighbour fits for each marker. |
meanfit |
Mean of the nearest neighbour fits over all markers. |
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