recalc.nnfit.from.map {MDSMap}

Calculate a nearest neighbour fit from an estimated map object.

Description

Calculates a new nearest neighbour fit based on a new order from a map object generated by calc.maps.pc, calc.maps.sphere or estimate.map

Usage

recalc.nnfit.from.map(estmap, mapobject, header = TRUE)

Arguments

estmap

A character string indicating the name of a comma separated value file with the first column containing marker names in the order of their estimated position.

mapobject

A map object generated by calc.maps.pc, calc.maps.sphere or estimate.map.

header

Logical argument indicating whether the .csv file estmap contains headers - default is TRUE

Details

Reads in a new estimated order, reorders the distance map and LOD scores by the new order and recalculates the nearest neighbour fit.

Value

A list with the elements:

fit

Sum over all markers of the nearest neighbour fits.

pointfits

The nearest neighbour fit for each marker.

meanfit

Meanv of the nearest neighbour fits over all markers.

See Also

calc.maps.pc, calc.maps.sphere, estimate.map, calc.nnfit