calc.nnfit {MDSMap}

Calculate the nearest neighbour fit.

Description

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.

Usage

calc.nnfit(distmap, lodmap, estmap)

Arguments

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 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.

Value

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.

See Also

calc.nnfit.loci