meandist.from.truth {MDSMap}

Calculates mean square distance between marker positions in two different maps.

Description

Calculates mean square distance of markers in the analysis from some objective "truth".

Usage

meandist.from.truth(estmap, realmap)

Arguments

estmap

Estimated map with 2 columns, name and position contain marker names and positions.

realmap

Map in which the first column contains marker names and the second contains marker positions. Column names are not necessary.

Details

The first column of realmap must contain identical entries to estmap$name. However, the order of entries can be different.

For every marker the difference between the position stated in estmap and in realmap is calculated (see get.dist.loci).

Every difference is squared and the mean of the square differences is returned.

Note that where different weights are used in estimating maps, it is valid to compare the mean distance from the truth. However, if different map functions are used then the distances are not comparable.

Therefore, if there is some knowledge of markers on a chromosome and data is simulated so that there is some objective knowledge of the truth then this function could be used to decide whether to use lod or lod2 weightings to estimate maps attempting to locate additional markers. However, it is not suitable for deciding on the map functions used to calculated the pairwise marker distances.

Value

A list with the following elements:

pointdist

Data frame containing marker names and the distance between the estimated position and the "real" position.

meansquaredist

mean square distance between the estimated real position of markers.