We have implemented a score test for linkage in Generalized Linear Mixed Models as an R program. It can deal with continuous, binary and count data. Arbitrary family structures are allowed and in the case of binary phenotypes both affected and unaffected individuals are taken into account. One important goal of the methodology is to be able to account for known population covariate effects when testing for linkage.
The program uses MERLIN for IBD computations so MERLIN should be accessible from R current directory. The actual input files are also in MERLIN format.
Citation: J. Lebrec and H. C. van Houwelingen. Score test for linkage in generalized linear models Hum Hered. 64:5-15 (2007)