I've just uploaded an R version of Daniel Schaid's 'haplo.score'
library
(from http://www.mayo.edu/statgen/) to CRAN.
>From the DESCRIPTION file:
[haplo.score is a] suite of routines that can be used to compute score
statistics to test associations between haplotypes and a wide variety of
traits, including binary, ordinal, quantitative, and Poisson. These methods
assume that all subjects are unrelated and that haplotypes are ambiguous
(due to unknown linkage phase of the genetic markers). The methods provide
several different global and
haplotype-specific tests for association, as well as provide adjustment for
non-genetic covariates and computation of simulation p-values (which may be
needed for sparse data).
Details on the background and theory of the score statistics can be found in
the following reference:
Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA.
Score tests for association of traits with haplotypes when
linkage phase is ambiguous. American J Human Genetics, February,
2002.
-Greg
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