This implementation of the score test for linkage is a package containing 6 compiled C programs.
The linkage analysis is performed in a three step procedure:
1) estimation of the variance of the proportions of alleles shared IBD by simulation (ibd.variance); 2) weight computation (GLM.weight, QTL.weight, AAO.weight or ARP.weight) and 3) computation of the final test statistic (score.test).
The four different weight computation programs are used for the following types of analysis:
- QTL.weight is used for performing a similar test to merlin regress with quantitative traits.
- ARP.weight is used for affected relative pairs linkage analysis.
- GLM.weight is used for performing linkage analysis with categorical and count data.
- AAO.weight is used for performing age at onset linkage analysis.
The programs use MERLIN for IBD computations so MERLIN should be accessible from the directory you want to run it in. The input files are also in MERLIN format.
For the manuals for each program see the separate readme files. The package contains Windows executables; the source code is available upon request.
- J. Lebrec and H.C. van Houwelingen. Score test for linkage in generalized linear models. Hum Hered. 64:5-15 (2007)
- A. Callegaro, H.C. van Houwelingen, and J.J Houwing-Duistermaat. Score test for age at onset genetic linkage analysis in selected sibling pairs. Stat Med. 28(14):1913-26 (2009)