linkage3p

An R package for evaluating the quality of a genetic map
by comparing the map order of any triple of markers
with experimental genotype data

by Sue Welham1,2 sue.welham@vsni.co.uk
Wally Gilks1,3 wally.gilks@maths.leeds.ac.uk
and Suzanne Clark1 suzanne.clark@rothamsted.ac.uk

1. Department of Computational and Systems Biology, Rothamsted Research, Harpenden, UK
2. VSN International Ltd, Hemel Hempstead, UK
3. Department of Statistics, University of Leeds, UK



This package implements a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure (Gilks, Welham, Wang, Clark and King, 2012). The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders.

Download R package:
linkage3p_1.0.tar.gz: tarred-gzipped file for Unix
linkage3p_1.0.zip: zipped file for Unix


References

Gilks, W.R., Welham, S.J., Wang, J., Clark, S.J. and King, G.J. (2012) Three-point appraisal of genetic linkage maps (submitted).