| calc.nnfit.loci {MDSMap} | R Documentation |
Calculates the nearest neighbour fit for an individual marker.
Description
Calculates the nearest neighbour fit for an individual marker.
Usage
calc.nnfit.loci(loci, distmap, lodmap, estmap)
Arguments
loci |
Scalar indicating the estimated rank position of the marker. |
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. |
Details
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 non zero. This function finds the nearest markers with a non-zero LOD score (this may be one or two markers). Calculates the estimated distances between these markers and the marker of interest and returns the sum of the absolute values of the difference between the observed and estimated distances.
Value
Scalar corresponding to the difference between the observed and estimated intermarker differences.