Linkage Explorer

by Wei-Min Chen

Copyright (C) Johns Hopkins University 

Bloomberg School of Public Health Department of Biostatistics

Linkage Explorer was developed to facilitate investigating problems in linkage analysis. A gene-mapper might find this software not really a competitor to a standard linkage program such as MERLIN or SOLAR, but LE can be of tremendous help for one to study nice features of modern methodologies in linkage analysis. It is written in C++ and its functions are versatile. In current version of LE, methods for quantitative traits have been well-implemented, on top of a kernel GEE routine. LE replicates key procedures in MERLIN-REGRESS, GeneHunter and SOLAR, which allows convenient comparisons among a variety of methods.

Functions of LinkageExplorer include: 1) simulation of small to middle sized pedigrees; 2) sample size and power calculation for classic linkage tests; 3) power analysis of dozens of linkage tests; 4) study of one particular data set (simulated from LE); etc.

This software is still being developed. Currently there is no software manual available. Commands are subject to change in the following versions. For questions and comments, you are welcome to contact Wei-Min Chen at wechen@umich.edu.  

LinkageExplorer (LE)  version 0.2.3, May 24, 2004

    Download LE for UNIX/Solaris

    Download LE for Windows & DOS

    Download LE for LINUX

Examples

    Download Example 1: linkage tests for normally distributed traits

    Download Example 2: robust linkage tests for non-normally distributed traits

    Download Example 3: pedigree simulation and a linkage analysis (for a linkage analysis, MERLIN is required to obtain multipoint IBD calculations)

    Download Example 4: pedigree simulation for a disease

Note: To run an example such as Example1, type in "le example1.le" in command line, or alternatively type in "run example1.le" inside LinkageExplorer.

Acknowledgements:

Many thanks to Dr. Kung-Yee Liang for his generous financial support during my Ph.D. studies, so that I might concentrate on writing this computer program and related theoretical research. Thanks to Dr. Karl Broman for his numerous comments on many improvements and thanks to Dr. Kung-Yee Liang for his insightful discussions. 

CITATION REFERENCE:

1. Chen WM, Broman KW, Liang KY (2004) Quantitative trait linkage analysis by generalized estimating equations: unification of variance components and Haseman-Elston regression. Genet Epidemiol May;26(4):265-272 [Abstract in PubMed] [131KB, in PDF format]

2. Chen WM, Broman KW, Liang KY (2004) Power and robustness of linkage tests for quantitative traits in general pedigrees (submitted)

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